MiMeDB: Showing metabocard for Pyridoxal 5'-phosphate (MMDBc0029660)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:36:29 UTC

Update Date

2024-09-29 14:59:15 UTC

Metabolite ID

MMDBc0029660

Metabolite Identification

Common Name

Pyridoxal 5'-phosphate

Description

Pyridoxal 5'-phosphate (PLP) is the active form of vitamin B6 serving as a coenzyme for reactions involving transamination, deamination, and decarboxylation. PLP also is necessary for the enzymatic reaction governing the release of glucose from glycogen. During transamination of amino acids, pyridoxal phosphate is transiently converted into pyridoxamine phosphate (pyridoxamine). -- It is the active form of vitamin B6 which comprises three natural organic compounds, pyridoxal, pyridoxamine and pyridoxine. -- Wikipedia

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

114
  Mrv1652309042000232D          

 16 16  0  0  0  0            999 V2000
    6.3799    0.2063    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.6655   -0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930    0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7925   -0.5082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0944    0.6188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075    1.4438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9674    0.9207    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220   -1.4438    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930   -1.4438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220    1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  0  0  0  0
  1  7  2  0  0  0  0
  2 11  1  0  0  0  0
  3 12  1  0  0  0  0
  6 16  2  0  0  0  0
  8 13  2  0  0  0  0
  8 14  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 14  2  0  0  0  0
 10 12  2  0  0  0  0
 10 16  1  0  0  0  0
 12 13  1  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029660

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=NC=C(COP(O)(O)=O)C(C=O)=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)

> <INCHI_KEY>
NGVDGCNFYWLIFO-UHFFFAOYSA-N

> <FORMULA>
C8H10NO6P

> <MOLECULAR_WEIGHT>
247.1419

> <EXACT_MASS>
247.024573569

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
20.898887181263255

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(4-formyl-5-hydroxy-6-methylpyridin-3-yl)methoxy]phosphonic acid

> <ALOGPS_LOGP>
-0.55

> <JCHEM_LOGP>
-2.0856087036128135

> <ALOGPS_LOGS>
-1.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.691277029499376

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.680298610655746

> <JCHEM_PKA_STRONGEST_BASIC>
4.109012435085948

> <JCHEM_POLAR_SURFACE_AREA>
116.95

> <JCHEM_REFRACTIVITY>
54.746300000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.70e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyridoxal phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 114                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  P   UNK     0      11.909   0.385   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0      10.576  -0.385   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       3.907   0.385   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      12.679  -0.949   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      13.243   1.155   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       5.241   2.695   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      11.139   1.719   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       6.574  -2.695   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       7.908  -0.385   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.574   0.385   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.242   0.385   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.241  -0.385   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.241  -1.925   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.908  -1.925   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.907  -2.695   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.574   1.925   0.000  0.00  0.00           C+0
CONECT    1    2    4    5    7                                             
CONECT    2    1   11                                                       
CONECT    3   12                                                            
CONECT    4    1                                                            
CONECT    5    1                                                            
CONECT    6   16                                                            
CONECT    7    1                                                            
CONECT    8   13   14                                                       
CONECT    9   10   11   14                                                  
CONECT   10    9   12   16                                                  
CONECT   11    2    9                                                       
CONECT   12    3   10   13                                                  
CONECT   13    8   12   15                                                  
CONECT   14    8    9                                                       
CONECT   15   13                                                            
CONECT   16    6   10                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

COMPND    HMDB0001491
HETATM    1  C1  UNL     1      -3.905  -1.496  -0.335  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.504  -0.954  -0.225  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.485  -1.803  -0.095  1.00  0.00           N  
HETATM    4  C3  UNL     1      -0.231  -1.333   0.004  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.077   0.014  -0.021  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.486   0.494   0.092  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.302  -0.608   0.214  1.00  0.00           O  
HETATM    8  P1  UNL     1       3.924  -0.235   0.351  1.00  0.00           P  
HETATM    9  O2  UNL     1       4.217   0.086   1.809  1.00  0.00           O  
HETATM   10  O3  UNL     1       4.824  -1.605  -0.104  1.00  0.00           O  
HETATM   11  O4  UNL     1       4.386   1.060  -0.624  1.00  0.00           O  
HETATM   12  C6  UNL     1      -0.983   0.887  -0.156  1.00  0.00           C  
HETATM   13  C7  UNL     1      -0.719   2.303  -0.188  1.00  0.00           C  
HETATM   14  O5  UNL     1      -1.699   3.114  -0.313  1.00  0.00           O  
HETATM   15  C8  UNL     1      -2.258   0.392  -0.256  1.00  0.00           C  
HETATM   16  O6  UNL     1      -3.339   1.275  -0.393  1.00  0.00           O  
HETATM   17  H1  UNL     1      -4.200  -1.427  -1.410  1.00  0.00           H  
HETATM   18  H2  UNL     1      -3.897  -2.572  -0.072  1.00  0.00           H  
HETATM   19  H3  UNL     1      -4.593  -0.928   0.328  1.00  0.00           H  
HETATM   20  H4  UNL     1       0.623  -2.006   0.112  1.00  0.00           H  
HETATM   21  H5  UNL     1       1.762   1.147  -0.760  1.00  0.00           H  
HETATM   22  H6  UNL     1       1.528   1.117   1.020  1.00  0.00           H  
HETATM   23  H7  UNL     1       4.274  -2.424   0.018  1.00  0.00           H  
HETATM   24  H8  UNL     1       4.437   1.870  -0.046  1.00  0.00           H  
HETATM   25  H9  UNL     1       0.259   2.708  -0.113  1.00  0.00           H  
HETATM   26  H10 UNL     1      -4.285   0.924  -0.468  1.00  0.00           H  
CONECT    1    2   17   18   19
CONECT    2    3    3   15
CONECT    3    4
CONECT    4    5    5   20
CONECT    5    6   12
CONECT    6    7   21   22
CONECT    7    8
CONECT    8    9    9   10   11
CONECT   10   23
CONECT   11   24
CONECT   12   13   15   15
CONECT   13   14   14   25
CONECT   15   16
CONECT   16   26
END

Synonyms

Value	Source
3-Hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinecarboxaldehyde	ChEBI
3-Hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde 5-phosphate	ChEBI
Codecarboxylase	ChEBI
Phosphoric acid mono-(4-formyl-5-hydroxy-6-methyl-pyridin-3-ylmethyl) ester	ChEBI
PLP	ChEBI
Pyridoxal 5'-(dihydrogen phosphate)	ChEBI
Pyridoxal 5-monophosphoric acid ester	ChEBI
Pyridoxal 5-phosphate	ChEBI
Pyridoxal phosphate	ChEBI
PYRIDOXAL-5'-phosphATE	ChEBI
3-Hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde 5-phosphoric acid	Generator
Phosphate mono-(4-formyl-5-hydroxy-6-methyl-pyridin-3-ylmethyl) ester	Generator
Pyridoxal 5'-(dihydrogen phosphoric acid)	Generator
Pyridoxal 5-monophosphate ester	Generator
Pyridoxal 5-phosphoric acid	Generator
Pyridoxal phosphoric acid	Generator
PYRIDOXAL-5'-phosphoric acid	Generator
Pyridoxal 5'-phosphoric acid	Generator
Apolon b6	HMDB
Biosechs	HMDB
Coenzyme b6	HMDB
Hairoxal	HMDB
Hexermin-p	HMDB
Hi-pyridoxin	HMDB
Hiadelon	HMDB
Himitan	HMDB
PAL-p	HMDB
Phosphopyridoxal	HMDB
Phosphopyridoxal coenzyme	HMDB
Pidopidon	HMDB
Piodel	HMDB
Pydoxal	HMDB
Pyridoxal p	HMDB
Pyridoxal-p	HMDB
Pyridoxyl phosphate	HMDB
Pyromijin	HMDB
Sechvitan	HMDB
Vitahexin-p	HMDB
Vitazechs	HMDB
Phosphate, pyridoxal	HMDB
Pyridoxal 5 phosphate	HMDB

Molecular Formula

C₈H₁₀NO₆P

Average Mass

247.1419

Monoisotopic Mass

247.024573569

IUPAC Name

[(4-formyl-5-hydroxy-6-methylpyridin-3-yl)methoxy]phosphonic acid

Traditional Name

pyridoxal phosphate

CAS Registry Number

54-47-7

SMILES

CC1=NC=C(COP(O)(O)=O)C(C=O)=C1O

InChI Identifier

InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)

InChI Key

NGVDGCNFYWLIFO-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridoxals and derivatives. Pyridoxals and derivatives are compounds containing a pyridoxal moiety, which consists of a pyridine ring substituted at positions 2,3,4, and 5 by a methyl group, a hydroxyl group, a carbaldehyde group, and a hydroxymethyl group, respectively.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Pyridine carboxaldehydes

Direct Parent

Pyridoxals and derivatives

Alternative Parents

Substituents

Pyridoxal
Aryl-aldehyde
Monoalkyl phosphate
Hydroxypyridine
Methylpyridine
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Vinylogous acid
Heteroaromatic compound
Azacycle
Organopnictogen compound
Aldehyde
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

monohydroxypyridine (CHEBI:18405 )
pyridinecarbaldehyde (CHEBI:18405 )
methylpyridines (CHEBI:18405 )
vitamin B6 phosphate (CHEBI:18405 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	5.7 g/L	ALOGPS
logP	-0.55	ALOGPS
logP	-2.1	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.68	ChemAxon
pKa (Strongest Basic)	4.11	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	116.95 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	54.75 m³·mol⁻¹	ChemAxon
Polarizability	20.9 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Mitochondria

Biospecimen Locations

Blood
Cerebrospinal Fluid (CSF)
Erythrocyte
Feces
Kidney
Liver
Neuron
Skeletal Muscle
Urine

Tissue Locations

Erythrocyte
Kidney
Liver
Neuron
Skeletal Muscle

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191693	5-aminolevulinate synthase, erythroid-specific, mitochondrial	Unknown	P22557	Homo sapiens
MMDBp0191698	5-aminolevulinate synthase, nonspecific, mitochondrial	Unknown	P13196	Homo sapiens
MMDBp0191723	2-amino-3-ketobutyrate coenzyme A ligase, mitochondrial	Enzyme	O75600	Homo sapiens
MMDBp0191859	Methylenetetrahydrofolate reductase	Unknown	P42898	Homo sapiens
MMDBp0191918	4-aminobutyrate aminotransferase, mitochondrial	Enzyme	P80404	Homo sapiens
MMDBp0191947	Tyrosine aminotransferase	Enzyme	P17735	Homo sapiens
MMDBp0191948	Aromatic-L-amino-acid decarboxylase	Enzyme	P20711	Homo sapiens
MMDBp0191953	Aspartate aminotransferase, cytoplasmic	Enzyme	P17174	Homo sapiens
MMDBp0191954	Aspartate aminotransferase, mitochondrial	Enzyme	P00505	Homo sapiens
MMDBp0191971	Branched-chain-amino-acid aminotransferase, cytosolic	Enzyme	P54687	Homo sapiens
MMDBp0191994	Kynureninase	Unknown	Q16719	Homo sapiens
MMDBp0191997	Glucose-6-phosphate 1-dehydrogenase	Enzyme	P11413	Homo sapiens
MMDBp0192037	Glycogen phosphorylase, liver form	Enzyme	P06737	Homo sapiens
MMDBp0192040	Glycogen phosphorylase, muscle form	Enzyme	P11217	Homo sapiens
MMDBp0192042	Glycogen phosphorylase, brain form	Enzyme	P11216	Homo sapiens
MMDBp0192045	Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial	Enzyme	Q8N5Z0	Homo sapiens
MMDBp0192063	Alanine--glyoxylate aminotransferase 2, mitochondrial	Enzyme	Q9BYV1	Homo sapiens
MMDBp0192067	Ornithine aminotransferase, mitochondrial	Enzyme	P04181	Homo sapiens
MMDBp0192123	Kynurenine--oxoglutarate transaminase 1	Enzyme	Q16773	Homo sapiens
MMDBp0192169	Branched-chain-amino-acid aminotransferase, mitochondrial	Enzyme	O15382	Homo sapiens
MMDBp0192186	Cystathionine gamma-lyase	Enzyme	P32929	Homo sapiens
MMDBp0192310	L-serine dehydratase/L-threonine deaminase	Enzyme	P20132	Homo sapiens
MMDBp0192313	Pyridoxine-5'-phosphate oxidase	Unknown	Q9NVS9	Homo sapiens
MMDBp0192325	Formimidoyltransferase-cyclodeaminase	Enzyme	O95954	Homo sapiens
MMDBp0192341	Glutamate decarboxylase 2	Enzyme	Q05329	Homo sapiens
MMDBp0192342	Glutamate decarboxylase 1	Enzyme	Q99259	Homo sapiens
MMDBp0192399	Cystathionine beta-synthase	Unknown	P35520	Homo sapiens
MMDBp0192409	Serine--pyruvate aminotransferase	Unknown	P21549	Homo sapiens
MMDBp0192412	Serine hydroxymethyltransferase, mitochondrial	Enzyme	P34897	Homo sapiens
MMDBp0192414	Serine hydroxymethyltransferase, cytosolic	Enzyme	P34896	Homo sapiens
MMDBp0192415	Glycine dehydrogenase [decarboxylating], mitochondrial	Enzyme	P23378	Homo sapiens
MMDBp0192470	Alanine aminotransferase 1	Enzyme	P24298	Homo sapiens
MMDBp0192471	Phosphoserine aminotransferase	Enzyme	Q9Y617	Homo sapiens
MMDBp0192503	Histidine decarboxylase	Enzyme	P19113	Homo sapiens
MMDBp0192504	Serine palmitoyltransferase 1	Enzyme	O15269	Homo sapiens
MMDBp0192506	Serine palmitoyltransferase 2	Enzyme	O15270	Homo sapiens
MMDBp0192554	Cysteine sulfinic acid decarboxylase	Enzyme	Q9Y600	Homo sapiens
MMDBp0192645	Ornithine decarboxylase	Enzyme	P11926	Homo sapiens
MMDBp0192661	Sphingosine-1-phosphate lyase 1	Enzyme	O95470	Homo sapiens
MMDBp0192664	Pyridoxal kinase	Unknown	O00764	Homo sapiens
MMDBp0193463	Arginine decarboxylase	Enzyme	Q96A70	Homo sapiens
MMDBp0193473	Phosphatidylserine decarboxylase proenzyme	Enzyme	Q9UG56	Homo sapiens
MMDBp0193562	Cysteine desulfurase, mitochondrial	Unknown	Q9Y697	Homo sapiens
MMDBp0193773	Proline synthase co-transcribed bacterial homolog protein	Enzyme	O94903	Homo sapiens
MMDBp0193784	Aminoadipate aminotransferase, isoform CRA_b	Enzyme	Q4W5N8	Homo sapiens
MMDBp0193905	Threonine synthase-like 1	Enzyme	Q8IYQ7	Homo sapiens
MMDBp0193917	Ethanolamine-phosphate phospho-lyase	Enzyme	Q8TBG4	Homo sapiens
MMDBp0193926	Alanine aminotransferase 2	Enzyme	Q8TD30	Homo sapiens
MMDBp0193940	Pyridoxal phosphate phosphatase	Unknown	Q96GD0	Homo sapiens
MMDBp0193983	Selenocysteine lyase	Enzyme	Q96I15	Homo sapiens
MMDBp0195556	Pyridoxal phosphate phosphatase PHOSPHO2	Unknown	Q8TCD6	Homo sapiens
MMDBp0195723	Putative aspartate aminotransferase, cytoplasmic 2	Enzyme	Q8NHS2	Homo sapiens
MMDBp0195724	5-phosphohydroxy-L-lysine phospho-lyase	Enzyme	Q8IUZ5	Homo sapiens
MMDBp0195725	Glutamate decarboxylase-like protein 1	Enzyme	Q6ZQY3	Homo sapiens
MMDBp0195726	Kynurenine--oxoglutarate transaminase 3	Enzyme	Q6YP21	Homo sapiens
MMDBp0195727	Molybdenum cofactor sulfurase	Enzyme	Q96EN8	Homo sapiens
MMDBp0195728	Pyridoxal-dependent decarboxylase domain-containing protein 1	Enzyme	Q6P996	Homo sapiens
MMDBp0195729	Pyridoxal-dependent decarboxylase domain-containing protein 2	Enzyme	Q6P474	Homo sapiens
MMDBp0195730	Serine dehydratase-like	Enzyme	Q96GA7	Homo sapiens
MMDBp0195731	O-phosphoseryl-tRNA(Sec) selenium transferase	Enzyme	Q9HD40	Homo sapiens
MMDBp0195732	Serine palmitoyltransferase 3	Enzyme	Q9NUV7	Homo sapiens
MMDBp0195733	Serine racemase	Enzyme	Q9GZT4	Homo sapiens
MMDBp0195734	Threonine synthase-like 2	Enzyme	Q86YJ6	Homo sapiens
MMDBp0195735	Tyrosine aminotransferase	Enzyme	A1L4G7	Homo sapiens
MMDBp0195736	Serine hydroxymethyltransferase	Enzyme	A8MYA6	Homo sapiens
MMDBp0195737	Aspartate aminotransferase	Enzyme	Q2TU84	Homo sapiens
MMDBp0195738	GAD1 protein	Enzyme	Q49AK1	Homo sapiens
MMDBp0195739	Serine hydroxymethyltransferase	Enzyme	Q53ET4	Homo sapiens
MMDBp0195740	Serine hydroxymethyltransferase	Enzyme	Q53ET7	Homo sapiens
MMDBp0195741	Dopa decarboxylase (Aromatic L-amino acid decarboxylase)	Enzyme	Q53Y41	Homo sapiens
MMDBp0195742	Phosphorylase	Enzyme	Q59GM9	Homo sapiens
MMDBp0195743	Serine hydroxymethyltransferase	Enzyme	Q5BJF5	Homo sapiens
MMDBp0195744	Serine hydroxymethyltransferase	Enzyme	Q5HYG8	Homo sapiens
MMDBp0195745	Aminolevulinate, delta-, synthase 1, isoform CRA_a	Enzyme	Q5JAM2	Homo sapiens
MMDBp0195746	Aminolevulinate, delta-, synthase 2	Enzyme	Q5JZF5	Homo sapiens
MMDBp0195747	Glutamate decarboxylase 2 (Pancreatic islets and brain, 65kDa)	Enzyme	Q5VZ29	Homo sapiens
MMDBp0195748	Glutamate decarboxylase 2 (Pancreatic islets and brain, 65kDa)	Enzyme	Q5VZ30	Homo sapiens
MMDBp0195749	Putative L-Dopa decarboxylase	Enzyme	Q5W5T9	Homo sapiens
MMDBp0195750	DDC protein	Enzyme	Q6IBS8	Homo sapiens
MMDBp0195751	CSAD protein	Enzyme	Q86V02	Homo sapiens
MMDBp0195752	PDXDC1 protein	Enzyme	Q86XE2	Homo sapiens
MMDBp0195753	Glutamate decarboxylase 1 (Brain, 67kDa)	Enzyme	Q8IVA8	Homo sapiens
MMDBp0195754	Aminolevulinate, delta-, synthase 2	Enzyme	Q8N6H3	Homo sapiens
MMDBp0195755	Phosphorylase	Enzyme	Q8TDG6	Homo sapiens
MMDBp0195756	P-selectin cytoplasmic tail-associated protein (PCAP)	Enzyme	Q96JQ3	Homo sapiens
MMDBp0195757	Glutamic acid decarboxylase	Enzyme	Q9UGI5	Homo sapiens
MMDBp0195758	Cysteine sulfinic acid decarboxylase, isoform CRA_c	Enzyme	Q9Y602	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018455	Pyridoxine 5'-phosphate	Hydrogen peroxide	Pyridoxine/pyridoxamine 5'-phosphate oxidase	Oxidation	PathBank	31602464
MMDBr0018456	Pyridoxal	Pyridoxal 5'-phosphate	Pyridoxine/pyridoxal/pyridoxamine kinase	Phosphorylation	PathBank	31602464
MMDBr0018457	Pyridoxamine 5'-phosphate	Hydrogen peroxide	Pyridoxine/pyridoxamine 5'-phosphate oxidase	Oxidation	PathBank	31602464
MMDBr0018461	Pyridoxal 5'-phosphate	4-amino-2-methyl-5-diphosphomethylpyrimidine	HMP-PP phosphatase	Dephosphorylation	PathBank	31602464
MMDBr0019956	Pyridoxine 5'-phosphate	Hydrogen peroxide	Unknown Protein		PathBank	31602464
MMDBr0019957	Pyridoxal	Pyridoxal 5'-phosphate	Unknown Protein		PathBank	31602464
MMDBr0019958	Pyridoxamine 5'-phosphate	Hydrogen peroxide	Unknown Protein		PathBank	31602464

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Celiac disease	Slight Increase	Association	Human Cerebrospinal Fluid (CSF)	HMDB	6182788
Hypophosphatasia	Increased	Association	Human Blood	HMDB	2079838
Rheumatoid arthritis		Association	Human Blood	HMDB	16277678

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	12	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Turkey ; Cattle ; Chicken ; River trout ; Sheep ; Dog	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	439	Human feces; Human pleural fluid plaque; Pig ; Human sputum; Human ; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Human supragingival plaque; Cattle ; Human stool; Catfish	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	452	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Turkey ; Cattle ; Chicken ; River trout ; Sheep ; Dog	Unknown; Metabolic reconstruction
Bacteria	Actinobacteria	15	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	163	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	133	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human supragingival plaque; Human subgingival plaque; Human gastric fluid; Human urine	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	3	Human feces	Metabolic reconstruction
Bacteria	Firmicutes	29	Human feces; Human pleural fluid plaque; Pig ; Human sputum; Human ; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Human supragingival plaque; Cattle ; Human stool; Catfish	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	9	Human feces; Human	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	6		Metabolic reconstruction
Bacteria	Candidatus melainabacteria	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Tenericutes	4	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	2	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	6	Human feces; Human saliva	Unknown
Bacteria/Eubacteria	Deinococcus-thermus	5
Bacteria/Eubacteria	Cyanobacteria	12	Human
Bacteria	nah	1
Archaea/Archaea	Crenarchaeota	20		Metabolic reconstruction
Archaea/Archaea	Euryarchaeota	36		Metabolic reconstruction
Bacteria/Eubacteria	Chloroflexi	9
Bacteria/Eubacteria	Dictyoglomi	2
Bacteria/Eubacteria	Chlamydiae	1	Human
Bacteria/Eubacteria	Thermotogae	9
Archaea/Archaea	Thaumarchaeota	2		Metabolic reconstruction
Archaea/Archaea	Korarchaeota	1
Bacteria/Eubacteria	Acidobacteria	2

Exposure Sources

Food Exposures

Other Exposures

Source Type	Data Source	Reference
General Exposome	U.S. Environmental Protection Agency	CompTox
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.00243	0.00138			uM	Adult (>18 years old)	Not Specified	celiac disease	HMDB	6182788
Human Cerebrospinal fluid (csf)	Detected and Quantified			0.00500	0.00600	uM	Children (1-13 years old)	Female	Epilepsy, early-onset, vitamin B6-dependent	HMDB	27912044
Human Blood	Detected and Quantified	0.251		0.0310	1.182	uM	Adult (>18 years old)	Both	Hypophosphatasia, infantile	HMDB	2079838
Human Blood	Detected and Quantified	1.59				uM	Children (1-13 years old)	Female	Odontohypophosphatasia	HMDB	23093139
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.0036				uM	Newborn (0-30 days old)	Not Specified	PNPO deficiency	HMDB	18294893
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.012				uM	Newborn (0-30 days old)	Not Specified	PNPO deficiency	HMDB	18294893
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.014				uM	Newborn (0-30 days old)	Not Specified	PNPO deficiency	HMDB	18294893
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.018				uM	Newborn (0-30 days old)	Not Specified	PNPO deficiency	HMDB	18294893
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.0119		0.0036	0.018	uM	Newborn (0-30 days old)	Not Specified	PNPO deficiency	HMDB	18294893
Human Blood	Detected and Quantified	0.024		0.019	0.031	uM	Adult (>18 years old)	Both	Rheumatoid arthritis	HMDB	16277678
Human Blood	Detected and Quantified	0.03				uM	Adult (>18 years old)	Female	Normal	HMDB	18230968
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.000972	0.000283			uM	Adult (>18 years old)	Not Specified	Normal	HMDB	6182788
Human Blood	Detected and Quantified	0.0047	0.00072			uM	Adult (>18 years old)	Both	Normal	HMDB	1783639
Human Cerebrospinal fluid (csf)	Detected and Quantified			0.0110	0.0340	uM	Children (1-13 years old)	Not Specified	Normal	HMDB	27912044
Human Blood	Detected and Quantified			0.0146	0.0728	uM	Children (1-13 years old)	Not Specified	Normal	HMDB	23093139
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.0207	0.0069			uM	Children (1-13 years old)	Not Specified	Normal	HMDB	18294893
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.0305	0.0111			uM	Children (1-13 years old)	Not Specified	Normal	HMDB	18294893
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.0312	0.0049			uM	Children (1-13 years old)	Not Specified	Normal	HMDB	18294893
Human Cerebrospinal fluid (csf)	Detected and Quantified			0.032	0.078	uM	Children (1-13 years old)	Not Specified	Normal	HMDB	18294893
Human Blood	Detected and Quantified	0.042		0.0076	1.26	uM	Adult (>18 years old)	Both	Normal	HMDB	15450810
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.0431	0.0193			uM	Infant (0-1 year old)	Not Specified	Normal	HMDB	18294893
Human Cerebrospinal fluid (csf)	Detected and Quantified			0.044	0.089	uM	Children (1-13 years old)	Not Specified	Normal	HMDB	18294893
Human Blood	Detected and Quantified	0.0451		0.00400	0.207	uM	Adult (>18 years old)	Both	Normal	HMDB	2079838
Human Blood	Detected and Quantified	0.046		0.035	0.06	uM	Adult (>18 years old)	Both	Normal	HMDB	16277678
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.0515	0.0166			uM	Newborn (0-30 days old)	Not Specified	Normal	HMDB	18294893
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.0531	0.0186			uM	Infant (0-1 year old)	Not Specified	Normal	HMDB	18294893
Human Blood	Detected and Quantified	0.0572	0.0193			uM	Adolescent (13-18 years old)	Female	Normal	HMDB	17349090
Human Blood	Detected and Quantified	0.0581	0.0176			uM	Adolescent (13-18 years old)	Male	Normal	HMDB	17349090
Human Cerebrospinal fluid (csf)	Detected and Quantified	0.0654	0.0173			uM	Infant (0-1 year old)	Not Specified	Normal	HMDB	18294893
Human Blood	Detected and Quantified	0.205	0.193			uM	Adult (>18 years old)	Male	Normal	HMDB	21346713
Human Blood	Detected and Quantified	0.056	0.042			uM	Newborn (0-30 days old)	Both	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Blood	Detected and Quantified	0.061	0.052			uM	Children (1-13 years old)	Both	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Blood	Detected and Quantified	0.068	0.015			uM	Adult (>18 years old)	Female	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Blood	Detected and Quantified	0.075	0.022			uM	Adult (>18 years old)	Male	Normal	HMDB	Geigy Scientific Tables, 8th Rev edition, pp. 130. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp. Basel, Switzerland c1981-1992.
Human Erythrocyte	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Kidney	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Liver	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Neuron	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Skeletal muscle	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	34986597
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057
Human Blood	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057

External Links

HMDB ID

HMDB0001491

DrugBank ID

DB00114

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

18405

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Akopov MA, Kagan ZS, Berezov TT, Filiptsev PIa: [Kinetics and thermodynamics of heat inactivation of L-threonine-L-serine dehydratase from human liver]. Biokhimiia. 1978 Nov;43(11):2027-32. [PubMed:737218 ]
Longhi RC, Fleisher LD, Tallan HH, Gaull GE: Cystathionine beta-synthase deficiency: a qualitative abnormality of the deficient enzyme modified by vitamin B6 therapy. Pediatr Res. 1977 Feb;11(2):100-3. doi: 10.1203/00006450-197702000-00003. [PubMed:840498 ]
Seki T: Combination treatment of high-dose pyridoxal phosphate and low-dose ACTH in children with West syndrome and related disorders. Jpn J Psychiatry Neurol. 1990 Jun;44(2):219-37. doi: 10.1111/j.1440-1819.1990.tb01401.x. [PubMed:1701836 ]
Lacour B, Parry C, Drueke T, Touam M, Kreis H, Bailly M, Durand D: Pyridoxal 5'-phosphate deficiency in uremic undialyzed, hemodialyzed, and non-uremic kidney transplant patients. Clin Chim Acta. 1983 Jan 24;127(2):205-15. doi: 10.1016/s0009-8981(83)80005-9. [PubMed:6337752 ]
Schuster K, Bailey LB, Cerda JJ, Gregory JF 3rd: Urinary 4-pyridoxic acid excretion in 24-hour versus random urine samples as a measurement of vitamin B6 status in humans. Am J Clin Nutr. 1984 Mar;39(3):466-70. doi: 10.1093/ajcn/39.3.466. [PubMed:6695847 ]
Heiskanen K, Kallio M, Salmenpera L, Siimes MA, Ruokonen I, Perheentupa J: Vitamin B-6 status during childhood: tracking from 2 months to 11 years of age. J Nutr. 1995 Dec;125(12):2985-92. doi: 10.1093/jn/125.12.2985. [PubMed:7500176 ]
Fonda ML: Vitamin B6 metabolism and binding to proteins in the blood of alcoholic and nonalcoholic men. Alcohol Clin Exp Res. 1993 Dec;17(6):1171-8. doi: 10.1111/j.1530-0277.1993.tb05223.x. [PubMed:8116826 ]
Heiskanen K, Siimes MA, Perheentupa J, Salmenpera L: Reference ranges for erythrocyte pyridoxal 5'-phosphate concentration and the erythrocyte aspartate transaminase stimulation test in lactating mothers and their infants. Am J Clin Nutr. 1994 Jun;59(6):1297-303. doi: 10.1093/ajcn/59.6.1297. [PubMed:8198054 ]
Descombes E, Hanck AB, Fellay G: Water soluble vitamins in chronic hemodialysis patients and need for supplementation. Kidney Int. 1993 Jun;43(6):1319-28. doi: 10.1038/ki.1993.185. [PubMed:8315945 ]
Heiskanen K, Siimes MA, Salmenpera L, Perheentupa J: Low vitamin B6 status associated with slow growth in healthy breast-fed infants. Pediatr Res. 1995 Nov;38(5):740-6. doi: 10.1203/00006450-199511000-00018. [PubMed:8552443 ]
Stolzenberg-Solomon RZ, Albanes D, Nieto FJ, Hartman TJ, Tangrea JA, Rautalahti M, Sehlub J, Virtamo J, Taylor PR: Pancreatic cancer risk and nutrition-related methyl-group availability indicators in male smokers. J Natl Cancer Inst. 1999 Mar 17;91(6):535-41. doi: 10.1093/jnci/91.6.535. [PubMed:10088624 ]
Iqbal SJ, Plaha DS, Linforth GH, Dalgleish R: Hypophosphatasia: diagnostic application of linked DNA markers in the dominantly inherited adult form. Clin Sci (Lond). 1999 Jul;97(1):73-8. [PubMed:10369796 ]
Selvaag E, Bohmer T, Benkestock K: Reduced serum concentrations of riboflavine and ascorbic acid, and blood thiamine pyrophosphate and pyridoxal-5-phosphate in geriatric patients with and without pressure sores. J Nutr Health Aging. 2002;6(1):75-7. [PubMed:11813090 ]
Huang YC, Lan PH, Cheng CH, Lee BJ, Kan MN: Vitamin B6 intakes and status of mechanically ventilated critically ill patients in Taiwan. Eur J Clin Nutr. 2002 May;56(5):387-92. doi: 10.1038/sj.ejcn.1601321. [PubMed:12001008 ]
Huang YC, Chang SJ, Chiu YT, Chang HH, Cheng CH: The status of plasma homocysteine and related B-vitamins in healthy young vegetarians and nonvegetarians. Eur J Nutr. 2003 Apr;42(2):84-90. doi: 10.1007/s00394-003-0387-5. [PubMed:12638029 ]
Chiang EP, Bagley PJ, Roubenoff R, Nadeau M, Selhub J: Plasma pyridoxal 5'-phosphate concentration is correlated with functional vitamin B-6 indices in patients with rheumatoid arthritis and marginal vitamin B-6 status. J Nutr. 2003 Apr;133(4):1056-9. doi: 10.1093/jn/133.4.1056. [PubMed:12672918 ]
Chiang EP, Bagley PJ, Selhub J, Nadeau M, Roubenoff R: Abnormal vitamin B(6) status is associated with severity of symptoms in patients with rheumatoid arthritis. Am J Med. 2003 Mar;114(4):283-7. doi: 10.1016/s0002-9343(02)01528-0. [PubMed:12681455 ]
Lee BJ, Huang MC, Chung LJ, Cheng CH, Lin KL, Su KH, Huang YC: Folic acid and vitamin B12 are more effective than vitamin B6 in lowering fasting plasma homocysteine concentration in patients with coronary artery disease. Eur J Clin Nutr. 2004 Mar;58(3):481-7. doi: 10.1038/sj.ejcn.1601834. [PubMed:14985687 ]
Huang YC, Chang HH, Huang SC, Cheng CH, Lee BJ, Cheng SY, Su KH: Plasma pyridoxal 5'-phosphate is a significant indicator of immune responses in the mechanically ventilated critically ill. Nutrition. 2005 Jul-Aug;21(7-8):779-85. doi: 10.1016/j.nut.2004.11.013. [PubMed:15975484 ]
Chiang EP, Selhub J, Bagley PJ, Dallal G, Roubenoff R: Pyridoxine supplementation corrects vitamin B6 deficiency but does not improve inflammation in patients with rheumatoid arthritis. Arthritis Res Ther. 2005;7(6):R1404-11. doi: 10.1186/ar1839. Epub 2005 Oct 14. [PubMed:16277693 ]

Showing metabocard for Pyridoxal 5'-phosphate (MMDBc0029660)

MOL for #<Metabolite:0x00005645ca1539a0>

3D MOL for #<Metabolite:0x00005645ca1539a0>

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PDB for #<Metabolite:0x00005645ca1539a0>

3D PDB for #<Metabolite:0x00005645ca1539a0>

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Structure for #<Metabolite:0x00005645ca1539a0>

3D Structure for #<Metabolite:0x00005645ca1539a0>