MiMeDB: Showing metabocard for 5-Amino-6-(5'-phosphoribitylamino)uracil (MMDBc0030310)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 00:02:48 UTC

Update Date

2022-08-31 17:43:31 UTC

Metabolite ID

MMDBc0030310

Metabolite Identification

Common Name

5-Amino-6-(5'-phosphoribitylamino)uracil

Description

5-Amino-6-(5'-phosphoribitylamino)uracil is an intermediate in Riboflavin metabolism. 5-Amino-6-(5'-phosphoribitylamino)uracil is the; 3rd to last step in the synthesis of 7-Hydroxy-6-methyl-8-ribityl lumazine and is converted from 5-Amino-6-(5'-phosphoribosylamino)uracil via the enzyme 5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193). It is then; converted to 4-(1-D-Ribitylamino)-5-amino-2,6-dihydroxypyrimidine via the enzyme Hydrolases (EC 3.1.3.- ).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231219482D          

 23 23  0  0  0  0            999 V2000
   10.6826   -9.1385    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   12.8260   -7.0760    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3970   -5.4260    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6826   -6.6635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6826   -8.3135    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6826   -9.9635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.8576   -9.1385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.5076   -9.1385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2549   -2.1260    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.6839   -4.6010    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8260   -4.6010    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.2549   -4.6010    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.9694   -3.3635    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.8260   -2.9510    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.1116   -6.6635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1116   -5.8385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3970   -7.0760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8260   -5.4260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3970   -7.9010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5404   -4.1885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5404   -3.3635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2549   -2.9510    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9694   -4.1885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  1  6  1  0  0  0  0
  1  7  1  0  0  0  0
  1  8  2  0  0  0  0
  2 15  1  0  0  0  0
  3 16  1  0  0  0  0
  4 17  1  0  0  0  0
  5 19  1  0  0  0  0
  9 22  2  0  0  0  0
 10 23  2  0  0  0  0
 11 18  1  0  0  0  0
 11 20  1  0  0  0  0
 12 20  1  0  0  0  0
 12 23  1  0  0  0  0
 13 22  1  0  0  0  0
 13 23  1  0  0  0  0
 14 21  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 16 18  1  0  0  0  0
 17 19  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030310

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=C(NCC(O)C(O)C(O)COP(O)(O)=O)NC(=O)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H17N4O9P/c10-5-7(12-9(18)13-8(5)17)11-1-3(14)6(16)4(15)2-22-23(19,20)21/h3-4,6,14-16H,1-2,10H2,(H2,19,20,21)(H3,11,12,13,17,18)

> <INCHI_KEY>
RQRINYISXYAZKL-UHFFFAOYSA-N

> <FORMULA>
C9H17N4O9P

> <MOLECULAR_WEIGHT>
356.2264

> <EXACT_MASS>
356.073314674

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
30.255208429004316

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
({5-[(5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl}oxy)phosphonic acid

> <ALOGPS_LOGP>
-2.49

> <JCHEM_LOGP>
-5.751996526974423

> <ALOGPS_LOGS>
-2.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.3539846455749975

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4914898899860298

> <JCHEM_PKA_STRONGEST_BASIC>
6.520324602692354

> <JCHEM_POLAR_SURFACE_AREA>
223.70000000000002

> <JCHEM_REFRACTIVITY>
82.3575

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.89e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{5-[(5-amino-2,6-dioxo-1,3-dihydropyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl}oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  P   UNK     0      19.941 -17.059   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0      23.942 -13.209   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      21.274 -10.129   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      19.941 -12.439   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      19.941 -15.519   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      19.941 -18.599   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      18.401 -17.059   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      21.481 -17.059   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      26.609  -3.969   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      29.277  -8.589   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0      23.942  -8.589   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      26.609  -8.589   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0      27.943  -6.279   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0      23.942  -5.509   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      22.608 -12.439   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      22.608 -10.899   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      21.274 -13.209   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      23.942 -10.129   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      21.274 -14.749   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      25.275  -7.819   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      25.275  -6.279   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      26.609  -5.509   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      27.943  -7.819   0.000  0.00  0.00           C+0
CONECT    1    5    6    7    8                                             
CONECT    2   15                                                            
CONECT    3   16                                                            
CONECT    4   17                                                            
CONECT    5    1   19                                                       
CONECT    6    1                                                            
CONECT    7    1                                                            
CONECT    8    1                                                            
CONECT    9   22                                                            
CONECT   10   23                                                            
CONECT   11   18   20                                                       
CONECT   12   20   23                                                       
CONECT   13   22   23                                                       
CONECT   14   21                                                            
CONECT   15    2   16   17                                                  
CONECT   16    3   15   18                                                  
CONECT   17    4   15   19                                                  
CONECT   18   11   16                                                       
CONECT   19    5   17                                                       
CONECT   20   11   12   21                                                  
CONECT   21   14   20   22                                                  
CONECT   22    9   13   21                                                  
CONECT   23   10   12   13                                                  
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

Synonyms

Value	Source
5-Amino-2,6-dioxy-4-(5'-phosphoribitylamino)pyrimidine	HMDB
5-Amino-6-(5-phosphoribitylamino)uracil	HMDB

Molecular Formula

C₉H₁₇N₄O₉P

Average Mass

356.2264

Monoisotopic Mass

356.073314674

IUPAC Name

({5-[(5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl}oxy)phosphonic acid

Traditional Name

{5-[(5-amino-2,6-dioxo-1,3-dihydropyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl}oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

NC1=C(NCC(O)C(O)C(O)COP(O)(O)=O)NC(=O)NC1=O

InChI Identifier

InChI=1S/C9H17N4O9P/c10-5-7(12-9(18)13-8(5)17)11-1-3(14)6(16)4(15)2-22-23(19,20)21/h3-4,6,14-16H,1-2,10H2,(H2,19,20,21)(H3,11,12,13,17,18)

InChI Key

RQRINYISXYAZKL-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharide phosphates

Alternative Parents

Substituents

Monosaccharide phosphate
Pentose monosaccharide
Aminopyrimidine
Pyrimidone
Secondary aliphatic/aromatic amine
Monoalkyl phosphate
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Vinylogous amide
Secondary alcohol
Urea
Lactam
Secondary amine
Organoheterocyclic compound
Azacycle
Polyol
Hydrocarbon derivative
Organonitrogen compound
Amine
Organopnictogen compound
Organic oxide
Organic nitrogen compound
Alcohol
Primary amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	2.89 g/L	ALOGPS
logP	-2.5	ALOGPS
logP	-5.8	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	1.49	ChemAxon
pKa (Strongest Basic)	6.52	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	223.7 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	82.36 m³·mol⁻¹	ChemAxon
Polarizability	30.26 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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
MMDBr0019047	5-Amino-6-(5'-phosphoribosylamino)uracil	5-Amino-6-(5'-phosphoribitylamino)uracil	Riboflavin biosynthesis protein RibD	Synthesis	PathBank	31602464
MMDBr0019050	5-Amino-6-(5'-phosphoribitylamino)uracil	5-Amino-6-ribitylamino uracil	5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB	Dephosphorylation	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

HMDB0003841

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023235

KNApSAcK ID

Not Available

Chemspider ID

326

KEGG Compound ID

C04454

BioCyc ID

CPD-1086

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

333

PDB ID

Not Available

ChEBI ID

18247

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 5-Amino-6-(5'-phosphoribitylamino)uracil (MMDBc0030310)

MOL for #<Metabolite:0x00005645c92b8c10>

3D MOL for #<Metabolite:0x00005645c92b8c10>

3D SDF for #<Metabolite:0x00005645c92b8c10>

3D-SDF for #<Metabolite:0x00005645c92b8c10>

PDB for #<Metabolite:0x00005645c92b8c10>

3D PDB for #<Metabolite:0x00005645c92b8c10>

SMILES for #<Metabolite:0x00005645c92b8c10>

INCHI for #<Metabolite:0x00005645c92b8c10>

Structure for #<Metabolite:0x00005645c92b8c10>

3D Structure for #<Metabolite:0x00005645c92b8c10>