MiMeDB: Showing metabocard for 5-amino-6-(5-phospho-D-ribosylamino)uracil (MMDBc0055552)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:58:43 UTC

Update Date

2022-08-12 20:09:24 UTC

Metabolite ID

MMDBc0055552

Metabolite Identification

Common Name

5-amino-6-(5-phospho-D-ribosylamino)uracil

Description

5-amino-6-(5-phospho-D-ribosylamino)uracil belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups. Based on a literature review very few articles have been published on 5-amino-6-(5-phospho-D-ribosylamino)uracil.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221582D          

 27 28  0  0  1  0            999 V2000
    3.4888   -1.5291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7041   -1.7840    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1661   -3.8173    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367   -1.2991    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3693   -1.7840    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3188   -3.1499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9866   -3.7311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6242   -2.5687    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8372   -2.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1694   -4.5710    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1393   -3.2361    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0168   -2.3962    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222   -2.9774    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367   -0.4741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5846   -1.5291    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4715   -4.3985    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.1728   -1.5563    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.6711   -1.5712    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414   -2.6108    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6315   -1.0416    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1019   -2.0811    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4492   -2.5687    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8865   -1.8262    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.8332   -0.9692    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3016   -0.9246    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7859   -2.3674    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9987   -3.3037    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  4  2  1  0  0  0  0
  5  4  1  0  0  0  0
  6  3  2  0  0  0  0
  7  3  1  0  0  0  0
  8  5  1  0  0  0  0
 10  3  1  0  0  0  0
 11  6  1  0  0  0  0
  8 11  1  1  0  0  0
 12  6  1  0  0  0  0
 12  9  2  0  0  0  0
 13  7  2  0  0  0  0
 13  9  1  0  0  0  0
  4 14  1  6  0  0  0
  5 15  1  6  0  0  0
 16  7  1  0  0  0  0
 17  9  1  0  0  0  0
 21  1  1  0  0  0  0
 22  2  1  0  0  0  0
 22  8  1  0  0  0  0
 23 18  1  0  0  0  0
 23 19  1  0  0  0  0
 23 20  2  0  0  0  0
 23 21  1  0  0  0  0
  2 24  1  6  0  0  0
  4 25  1  1  0  0  0
  5 26  1  1  0  0  0
  8 27  1  6  0  0  0
M  CHG  2  16  -1  17  -1
M  END


  Mrv1652306172221582D          

 27 28  0  0  1  0            999 V2000
    3.4888   -1.5291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7041   -1.7840    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1661   -3.8173    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367   -1.2991    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3693   -1.7840    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3188   -3.1499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9866   -3.7311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6242   -2.5687    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8372   -2.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1694   -4.5710    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1393   -3.2361    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0168   -2.3962    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222   -2.9774    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367   -0.4741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5846   -1.5291    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4715   -4.3985    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.1728   -1.5563    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.6711   -1.5712    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414   -2.6108    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6315   -1.0416    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1019   -2.0811    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4492   -2.5687    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8865   -1.8262    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.8332   -0.9692    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3016   -0.9246    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7859   -2.3674    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9987   -3.3037    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  4  2  1  0  0  0  0
  5  4  1  0  0  0  0
  6  3  2  0  0  0  0
  7  3  1  0  0  0  0
  8  5  1  0  0  0  0
 10  3  1  0  0  0  0
 11  6  1  0  0  0  0
  8 11  1  1  0  0  0
 12  6  1  0  0  0  0
 12  9  2  0  0  0  0
 13  7  2  0  0  0  0
 13  9  1  0  0  0  0
  4 14  1  6  0  0  0
  5 15  1  6  0  0  0
 16  7  1  0  0  0  0
 17  9  1  0  0  0  0
 21  1  1  0  0  0  0
 22  2  1  0  0  0  0
 22  8  1  0  0  0  0
 23 18  1  0  0  0  0
 23 19  1  0  0  0  0
 23 20  2  0  0  0  0
 23 21  1  0  0  0  0
  2 24  1  6  0  0  0
  4 25  1  1  0  0  0
  5 26  1  1  0  0  0
  8 27  1  6  0  0  0
M  CHG  2  16  -1  17  -1
M  END
> <DATABASE_ID>
MMDBc0055552

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(O)[C@@]([H])(O)[C@]([H])(NC2=C(N)C([O-])=NC([O-])=N2)O[C@]1([H])COP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H15N4O9P/c10-3-6(12-9(17)13-7(3)16)11-8-5(15)4(14)2(22-8)1-21-23(18,19)20/h2,4-5,8,14-15H,1,10H2,(H2,18,19,20)(H3,11,12,13,16,17)/p-2/t2-,4-,5-,8-/m1/s1

> <INCHI_KEY>
LZEXYCAGPMYXLX-UMMCILCDSA-L

> <FORMULA>
C9H13N4O9P

> <MOLECULAR_WEIGHT>
352.197

> <EXACT_MASS>
352.043112172

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
28.855738795650282

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-amino-6-{[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]amino}pyrimidine-2,4-bis(olate)

> <JCHEM_LOGP>
-2.2255147968621434

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
1.2696273822499857

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.2099366998094947

> <JCHEM_PKA_STRONGEST_BASIC>
6.25139487307998

> <JCHEM_POLAR_SURFACE_AREA>
226.39999999999995

> <JCHEM_REFRACTIVITY>
95.8244

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
5-amino-6-{[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]amino}pyrimidine-2,4-bis(olate)

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       6.512  -2.854   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.048  -3.330   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.310  -7.126   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.802  -2.425   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.556  -3.330   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.595  -5.880   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.842  -6.965   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.032  -4.795   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.563  -4.312   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.316  -8.532   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       2.127  -6.041   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      -0.031  -4.473   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0      -2.468  -5.558   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       3.802  -0.885   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.091  -2.854   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -2.747  -8.211   0.000  0.00  0.00           O-1
HETATM   17  O   UNK     0      -2.189  -2.905   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0      10.586  -2.933   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       9.597  -4.874   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       8.646  -1.944   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       7.657  -3.885   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.572  -4.795   0.000  0.00  0.00           O+0
HETATM   23  P   UNK     0       9.121  -3.409   0.000  0.00  0.00           P+0
HETATM   24  H   UNK     0       5.289  -1.809   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       2.430  -1.726   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       1.467  -4.419   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       3.731  -6.167   0.000  0.00  0.00           H+0
CONECT    1    2   21                                                       
CONECT    2    1    4   22   24                                             
CONECT    3    6    7   10                                                  
CONECT    4    2    5   14   25                                             
CONECT    5    4    8   15   26                                             
CONECT    6    3   11   12                                                  
CONECT    7    3   13   16                                                  
CONECT    8    5   11   22   27                                             
CONECT    9   12   13   17                                                  
CONECT   10    3                                                            
CONECT   11    6    8                                                       
CONECT   12    6    9                                                       
CONECT   13    7    9                                                       
CONECT   14    4                                                            
CONECT   15    5                                                            
CONECT   16    7                                                            
CONECT   17    9                                                            
CONECT   18   23                                                            
CONECT   19   23                                                            
CONECT   20   23                                                            
CONECT   21    1   23                                                       
CONECT   22    2    8                                                       
CONECT   23   18   19   20   21                                             
CONECT   24    2                                                            
CONECT   25    4                                                            
CONECT   26    5                                                            
CONECT   27    8                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   56    0
END

Synonyms

Value	Source
5-Amino-6-(5-phosphoribosylamino)uracil dianion	ChEBI

Molecular Formula

C₉H₁₃N₄O₉P

Average Mass

352.197

Monoisotopic Mass

352.043112172

IUPAC Name

5-amino-6-{[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]amino}pyrimidine-2,4-bis(olate)

Traditional Name

5-amino-6-{[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]amino}pyrimidine-2,4-bis(olate)

CAS Registry Number

Not Available

SMILES

[H][C@]1(O)[C@@]([H])(O)[C@]([H])(NC2=C(N)C([O-])=NC([O-])=N2)O[C@]1([H])COP(O)(O)=O

InChI Identifier

InChI=1S/C9H15N4O9P/c10-3-6(12-9(17)13-7(3)16)11-8-5(15)4(14)2(22-8)1-21-23(18,19)20/h2,4-5,8,14-15H,1,10H2,(H2,18,19,20)(H3,11,12,13,16,17)/p-2/t2-,4-,5-,8-/m1/s1

InChI Key

LZEXYCAGPMYXLX-UMMCILCDSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Aminopyrimidine
Pyrimidone
Secondary aliphatic/aromatic amine
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Urea
Secondary alcohol
Lactam
1,2-diol
Secondary amine
Oxacycle
Azacycle
Organoheterocyclic compound
Alcohol
Primary amine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Amine
Organonitrogen compound
Organic nitrogen compound
Organic anion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

organophosphate oxoanion (CHEBI:58453 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-2.2	ChemAxon
pKa (Strongest Acidic)	0.21	ChemAxon
pKa (Strongest Basic)	6.25	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	226.4 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	95.82 m³·mol⁻¹	ChemAxon
Polarizability	28.86 Å³	ChemAxon
Number of Rings	2	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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0013692	5-Amino-6-(5-phospho-D-ribitylamino)uracil	5-amino-6-(5-phospho-D-ribosylamino)uracil	Riboflavin biosynthesis protein RibD	Reduction	RHEA	34755880
MMDBr0013693	5-Amino-6-(5-phospho-D-ribitylamino)uracil	5-amino-6-(5-phospho-D-ribosylamino)uracil	Riboflavin biosynthesis protein RibD	Synthesis	RHEA	34755880
MMDBr0016770	5-amino-6-(5-phospho-D-ribosylamino)uracil	5,6-diaminouracil	N-glycosidase YbiA	Synthesis	RHEA	34755880
MMDBr0024696	Water	Ammonium	Riboflavin biosynthesis protein RibD	Synthesis	RHEA	34755880
MMDBr0024697	Water	Ammonium	Riboflavin biosynthesis protein RibD	Synthesis	RHEA	34755880

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
Bacteria	Proteobacteria	11	Human feces; Human
Bacteria	Aquificae	1
Bacteria	Firmicutes	2	Human ; Human feces
Bacteria	Chlamydiae	3	Human
Bacteria	Actinobacteria	3	Human
Bacteria	nah	1
Viruses/Bamfordvirae	Nucleocytoviricota	1
Bacteria	Cyanobacteria	1

Exposure Sources

Source Type	Source Sub-type	Species	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

26333186

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25245199

PDB ID

Not Available

ChEBI ID

58453

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 5-amino-6-(5-phospho-D-ribosylamino)uracil (MMDBc0055552)

MOL for #<Metabolite:0x00007fe2ac0906f0>

3D MOL for #<Metabolite:0x00007fe2ac0906f0>

3D SDF for #<Metabolite:0x00007fe2ac0906f0>

3D-SDF for #<Metabolite:0x00007fe2ac0906f0>

PDB for #<Metabolite:0x00007fe2ac0906f0>

3D PDB for #<Metabolite:0x00007fe2ac0906f0>

SMILES for #<Metabolite:0x00007fe2ac0906f0>

INCHI for #<Metabolite:0x00007fe2ac0906f0>

Structure for #<Metabolite:0x00007fe2ac0906f0>

3D Structure for #<Metabolite:0x00007fe2ac0906f0>