MiMeDB: Showing metabocard for D-Erythro-imidazole-glycerol-phosphate (MMDBc0029922)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:46:58 UTC

Update Date

2022-08-31 17:37:39 UTC

Metabolite ID

MMDBc0029922

Metabolite Identification

Common Name

D-Erythro-imidazole-glycerol-phosphate

Description

D-Erythro-imidazole-glycerol-phosphate is an intermediate in Histidine metabolism. It is a substrate for imidazoleglycerol-phosphate dehydratase (hisB) and can be generated from Phosphoribulosyl-formimino-AICAR-phosphate then it is converted to Imidazole-acetol phosphate.

Structure

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


  Mrv1652309042000352D          

 15 15  0  0  0  0            999 V2000
 9999.234310000.2012    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.9491 9999.7893    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.234310001.0259    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.663110000.2012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.9491 9998.9640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.3785 9999.7893    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.093910000.2012    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10001.681510000.9166    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.8072 9999.7893    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.506210000.9166    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.847710000.2837    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9997.1803 9999.7987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.4352 9999.0141    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2602 9999.0141    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5151 9999.7987    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  6  0  0  0
  2  4  1  0  0  0  0
  2  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  7 10  1  0  0  0  0
 14 15  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 11 12  2  0  0  0  0
 11 15  1  0  0  0  0
  1 15  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029922

> <DATABASE_NAME>
MIME

> <SMILES>
O[C@H](COP(O)(O)=O)[C@@H](O)C1=CNC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C6H11N2O6P/c9-5(2-14-15(11,12)13)6(10)4-1-7-3-8-4/h1,3,5-6,9-10H,2H2,(H,7,8)(H2,11,12,13)/t5-,6+/m1/s1

> <INCHI_KEY>
HFYBTHCYPKEDQQ-RITPCOANSA-N

> <FORMULA>
C6H11N2O6P

> <MOLECULAR_WEIGHT>
238.1351

> <EXACT_MASS>
238.035472606

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
19.78655716370441

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S)-2,3-dihydroxy-3-(1H-imidazol-4-yl)propoxy]phosphonic acid

> <ALOGPS_LOGP>
-1.59

> <JCHEM_LOGP>
-4.2779145684391855

> <ALOGPS_LOGS>
-1.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.5993663135356275

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.482402993615492

> <JCHEM_PKA_STRONGEST_BASIC>
5.78529472668903

> <JCHEM_POLAR_SURFACE_AREA>
135.9

> <JCHEM_REFRACTIVITY>
48.1795

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.22e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S)-2,3-dihydroxy-3-(1H-imidazol-4-yl)propoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0    8665.2378667.042   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8666.5728666.273   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0    8665.2378668.582   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0    8667.9048667.042   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8666.5728664.733   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8669.2408666.273   0.000  0.00  0.00           O+0
HETATM    7  P   UNK     0    8670.5758667.042   0.000  0.00  0.00           P+0
HETATM    8  O   UNK     0    8669.8058668.378   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0    8671.9078666.273   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8671.3458668.378   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0    8662.6498667.196   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0    8661.4038666.291   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0    8661.8798664.826   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0    8663.4198664.826   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8663.8958666.291   0.000  0.00  0.00           C+0
CONECT    1    2    3   15                                                  
CONECT    2    1    4    5                                                  
CONECT    3    1                                                            
CONECT    4    2    6                                                       
CONECT    5    2                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8    9   10                                             
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    7                                                            
CONECT   11   12   15                                                       
CONECT   12   13   11                                                       
CONECT   13   12   14                                                       
CONECT   14   15   13                                                       
CONECT   15   14   11    1                                                  
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

COMPND    HMDB0012208
HETATM    1  O1  UNL     1       3.606  -1.112  -1.297  1.00  0.00           O  
HETATM    2  P1  UNL     1       3.609  -0.062  -0.184  1.00  0.00           P  
HETATM    3  O2  UNL     1       4.415   1.310  -0.734  1.00  0.00           O  
HETATM    4  O3  UNL     1       4.410  -0.741   1.136  1.00  0.00           O  
HETATM    5  O4  UNL     1       2.003   0.253   0.200  1.00  0.00           O  
HETATM    6  C1  UNL     1       1.391  -0.989   0.460  1.00  0.00           C  
HETATM    7  C2  UNL     1      -0.056  -0.670   0.803  1.00  0.00           C  
HETATM    8  O5  UNL     1      -0.099   0.153   1.913  1.00  0.00           O  
HETATM    9  C3  UNL     1      -0.645   0.015  -0.426  1.00  0.00           C  
HETATM   10  O6  UNL     1      -0.566  -0.873  -1.494  1.00  0.00           O  
HETATM   11  C4  UNL     1      -2.033   0.447  -0.220  1.00  0.00           C  
HETATM   12  C5  UNL     1      -3.157  -0.358  -0.215  1.00  0.00           C  
HETATM   13  N1  UNL     1      -4.230   0.440   0.009  1.00  0.00           N  
HETATM   14  C6  UNL     1      -3.796   1.713   0.141  1.00  0.00           C  
HETATM   15  N2  UNL     1      -2.467   1.703   0.001  1.00  0.00           N  
HETATM   16  H1  UNL     1       3.865   2.127  -0.712  1.00  0.00           H  
HETATM   17  H2  UNL     1       4.001  -0.417   1.978  1.00  0.00           H  
HETATM   18  H3  UNL     1       1.903  -1.515   1.295  1.00  0.00           H  
HETATM   19  H4  UNL     1       1.383  -1.564  -0.482  1.00  0.00           H  
HETATM   20  H5  UNL     1      -0.638  -1.595   0.985  1.00  0.00           H  
HETATM   21  H6  UNL     1       0.724   0.111   2.471  1.00  0.00           H  
HETATM   22  H7  UNL     1      -0.012   0.907  -0.663  1.00  0.00           H  
HETATM   23  H8  UNL     1      -0.726  -0.454  -2.360  1.00  0.00           H  
HETATM   24  H9  UNL     1      -3.222  -1.441  -0.360  1.00  0.00           H  
HETATM   25  H10 UNL     1      -5.211   0.073   0.060  1.00  0.00           H  
HETATM   26  H11 UNL     1      -4.452   2.539   0.325  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4    5
CONECT    3   16
CONECT    4   17
CONECT    5    6
CONECT    6    7   18   19
CONECT    7    8    9   20
CONECT    8   21
CONECT    9   10   11   22
CONECT   10   23
CONECT   11   12   12   15
CONECT   12   13   24
CONECT   13   14   25
CONECT   14   15   15   26
END

Synonyms

Value	Source
D-Erythro-imidazole-glycerol 3-phosphate	ChEBI
D-Erythro-imidazole-glycerol phosphate	ChEBI
D-Erythro-imidazole-glycerol 3-phosphoric acid	Generator
D-Erythro-imidazole-glycerol phosphoric acid	Generator
D-Erythro-imidazole-glycerol-phosphoric acid	Generator
D-erythro-1-(Imidazol-4-yl)glycerol 3-phosphate	HMDB
D-erythro-Imidazoleglycerol-phosphate	HMDB
D-erythro-Imidazole-glycerol-P	HMDB
D-erythro-Imidazole-glycerol-phosphate	HMDB
D-erythro-Imidazolylglycerol phosphate	HMDB
IGP	HMDB
Imidazole glycerol phosphate	HMDB
erythro-Imidazole-glycerol-P	HMDB
erythro-Imidazole-glycerol-phosphate	HMDB

Molecular Formula

C₆H₁₁N₂O₆P

Average Mass

238.1351

Monoisotopic Mass

238.035472606

IUPAC Name

[(2R,3S)-2,3-dihydroxy-3-(1H-imidazol-4-yl)propoxy]phosphonic acid

Traditional Name

(2R,3S)-2,3-dihydroxy-3-(1H-imidazol-4-yl)propoxyphosphonic acid

CAS Registry Number

36244-87-8

SMILES

O[C@H](COP(O)(O)=O)[C@@H](O)C1=CNC=N1

InChI Identifier

InChI=1S/C6H11N2O6P/c9-5(2-14-15(11,12)13)6(10)4-1-7-3-8-4/h1,3,5-6,9-10H,2H2,(H,7,8)(H2,11,12,13)/t5-,6+/m1/s1

InChI Key

HFYBTHCYPKEDQQ-RITPCOANSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Organic phosphoric acids and derivatives

Sub Class

Phosphate esters

Direct Parent

Monoalkyl phosphates

Alternative Parents

Substituents

Monoalkyl phosphate
Azole
Imidazole
Heteroaromatic compound
Secondary alcohol
1,2-diol
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic nitrogen compound
Aromatic alcohol
Organooxygen compound
Organonitrogen compound
Alcohol
Organic oxide
Organopnictogen compound
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

imidazoles (CHEBI:17805 )
sn-glycerol 3-phosphates (CHEBI:17805 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	22.2 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-4.3	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	1.48	ChemAxon
pKa (Strongest Basic)	5.79	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	135.9 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	48.18 m³·mol⁻¹	ChemAxon
Polarizability	19.79 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

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018256	L-Glutamine	L-Glutamic acid	Imidazole glycerol phosphate synthase subunit HisH	Synthesis	PathBank	31602464
MMDBr0018257	D-Erythro-imidazole-glycerol-phosphate	Imidazole acetol-phosphate	Histidine biosynthesis bifunctional protein HisB	Synthesis	PathBank	31602464
MMDBr0019577	L-Glutamine	L-Glutamic acid	Imidazole glycerol phosphate synthase hisHF	Synthesis	PathBank	31602464
MMDBr0019578	D-Erythro-imidazole-glycerol-phosphate	Imidazole acetol-phosphate	Imidazoleglycerol-phosphate dehydratase	Hydration/dehydration of C-O bond	PathBank	31602464

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

HMDB0012208

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

D-ERYTHRO-IMIDAZOLE-GLYCEROL-P

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440431

PDB ID

Not Available

ChEBI ID

17805

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for D-Erythro-imidazole-glycerol-phosphate (MMDBc0029922)

MOL for #<Metabolite:0x00005645c9bde2b8>

3D MOL for #<Metabolite:0x00005645c9bde2b8>

3D SDF for #<Metabolite:0x00005645c9bde2b8>

3D-SDF for #<Metabolite:0x00005645c9bde2b8>

PDB for #<Metabolite:0x00005645c9bde2b8>

3D PDB for #<Metabolite:0x00005645c9bde2b8>

SMILES for #<Metabolite:0x00005645c9bde2b8>

INCHI for #<Metabolite:0x00005645c9bde2b8>

Structure for #<Metabolite:0x00005645c9bde2b8>

3D Structure for #<Metabolite:0x00005645c9bde2b8>