MiMeDB: Showing metabocard for 2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine (MMDBc0029772)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:41:03 UTC

Update Date

2022-08-31 17:16:50 UTC

Metabolite ID

MMDBc0029772

Metabolite Identification

Common Name

2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine

Description

2,5-Diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine or DARP, is an intermediate in flavin biosynthesis. It is a substrate for diaminohydroxyphosphoribosylaminopyrimidine deaminase, which catalyzes the reaction 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + H2O = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NH3

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 10231218322D          

 28 29  0  0  0  0            999 V2000
   -0.3715   -0.4672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7041   -1.7840    0.0000 C   0  0  1  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
    2.4492   -2.5687    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4131   -0.7221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5430    0.3398    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3693   -1.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9341   -3.2361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8547    0.6369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9846   -1.0192    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4678    1.1889    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5846   -1.5291    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0262   -0.1701    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0701    0.8918    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4888   -1.5291    0.0000 O   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
   -1.3277    0.5947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5986   -3.9898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5751   -3.0636    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8408   -3.9703    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6684   -2.3294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6242   -2.5687    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7546   -3.1499    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.5467   -0.9742    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5994   -0.6957    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2641   -2.4396    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2402   -0.9692    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1136   -3.3223    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  2  0  0  0  0
  6  1  1  0  0  0  0
  7  3  1  0  0  0  0
  4  8  1  1  0  0  0
 10  1  1  0  0  0  0
 11  9  2  0  0  0  0
 12  5  1  0  0  0  0
 12  7  1  0  0  0  0
 13  5  1  0  0  0  0
 13  9  1  0  0  0  0
 14  6  2  0  0  0  0
 14  9  1  0  0  0  0
  2 15  1  6  0  0  0
  3 16  1  6  0  0  0
 17  6  1  0  0  0  0
 18  8  1  0  0  0  0
 22  4  1  0  0  0  0
 22  7  1  0  0  0  0
 23  8  1  0  0  0  0
 23 19  1  0  0  0  0
 23 20  1  0  0  0  0
 23 21  2  0  0  0  0
  2 24  1  1  0  0  0
  3 25  1  1  0  0  0
  4 26  1  6  0  0  0
 27  7  1  0  0  0  0
 28  8  1  0  0  0  0
M  END


  Mrv0541 10231218322D          

 28 29  0  0  0  0            999 V2000
   -0.3715   -0.4672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7041   -1.7840    0.0000 C   0  0  1  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
    2.4492   -2.5687    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4131   -0.7221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5430    0.3398    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3693   -1.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9341   -3.2361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8547    0.6369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9846   -1.0192    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4678    1.1889    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5846   -1.5291    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0262   -0.1701    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0701    0.8918    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4888   -1.5291    0.0000 O   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
   -1.3277    0.5947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5986   -3.9898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5751   -3.0636    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8408   -3.9703    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6684   -2.3294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6242   -2.5687    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7546   -3.1499    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.5467   -0.9742    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5994   -0.6957    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2641   -2.4396    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2402   -0.9692    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1136   -3.3223    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  2  0  0  0  0
  6  1  1  0  0  0  0
  7  3  1  0  0  0  0
  4  8  1  1  0  0  0
 10  1  1  0  0  0  0
 11  9  2  0  0  0  0
 12  5  1  0  0  0  0
 12  7  1  0  0  0  0
 13  5  1  0  0  0  0
 13  9  1  0  0  0  0
 14  6  2  0  0  0  0
 14  9  1  0  0  0  0
  2 15  1  6  0  0  0
  3 16  1  6  0  0  0
 17  6  1  0  0  0  0
 18  8  1  0  0  0  0
 22  4  1  0  0  0  0
 22  7  1  0  0  0  0
 23  8  1  0  0  0  0
 23 19  1  0  0  0  0
 23 20  1  0  0  0  0
 23 21  2  0  0  0  0
  2 24  1  1  0  0  0
  3 25  1  1  0  0  0
  4 26  1  6  0  0  0
 27  7  1  0  0  0  0
 28  8  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029772

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H16N5O8P/c10-1-5(13-9(11)14-6(1)17)12-7-3(16)2(15)4(22-7)8(18)23(19,20)21/h2-4,7-8,15-16,18H,10H2,(H2,19,20,21)(H4,11,12,13,14,17)/t2-,3+,4-,7?,8?/m0/s1

> <INCHI_KEY>
CIEXRWBOBYOQGW-DOAYSINJSA-N

> <FORMULA>
C9H16N5O8P

> <MOLECULAR_WEIGHT>
353.2258

> <EXACT_MASS>
353.073649025

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
30.007162891454186

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2S,3S,4R)-5-[(5-amino-6-hydroxy-2-imino-2,3-dihydropyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl](hydroxy)methyl}phosphonic acid

> <ALOGPS_LOGP>
-2.57

> <JCHEM_LOGP>
-4.434789593777724

> <ALOGPS_LOGS>
-1.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
1.7245205126871226

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2523010134216186

> <JCHEM_PKA_STRONGEST_BASIC>
21.88602730358451

> <JCHEM_POLAR_SURFACE_AREA>
233.96999999999997

> <JCHEM_REFRACTIVITY>
92.40949999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.36e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2S,3S,4R)-5-[(5-amino-6-hydroxy-2-imino-3H-pyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl](hydroxy)methylphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-OCT-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   23  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   24  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    5    6   10                                                  
CONECT    2    3    4   15   24                                             
CONECT    3    2    7   16   25                                             
CONECT    4    2    8   22   26                                             
CONECT    5    1   12   13                                                  
CONECT    6    1   14   17                                                  
CONECT    7    3   12   22   27                                             
CONECT    8    4   18   23   28                                             
CONECT    9   11   13   14                                                  
CONECT   10    1                                                            
CONECT   11    9                                                            
CONECT   12    5    7                                                       
CONECT   13    5    9                                                       
CONECT   14    6    9                                                       
CONECT   15    2                                                            
CONECT   16    3                                                            
CONECT   17    6                                                            
CONECT   18    8                                                            
CONECT   19   23                                                            
CONECT   20   23                                                            
CONECT   21   23                                                            
CONECT   22    4    7                                                       
CONECT   23    8   19   20   21                                             
CONECT   24    2                                                            
CONECT   25    3                                                            
CONECT   26    4                                                            
CONECT   27    7                                                            
CONECT   28    8                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   58    0
END

Synonyms

Not Available

Molecular Formula

C₉H₁₆N₅O₈P

Average Mass

353.2258

Monoisotopic Mass

353.073649025

IUPAC Name

{[(2S,3S,4R)-5-[(5-amino-6-hydroxy-2-imino-2,3-dihydropyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl](hydroxy)methyl}phosphonic acid

Traditional Name

[(2S,3S,4R)-5-[(5-amino-6-hydroxy-2-imino-3H-pyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl](hydroxy)methylphosphonic acid

CAS Registry Number

Not Available

SMILES

[H]C(O)([C@@]1([H])OC([H])(NC2=C(N)C(O)=NC(=N)N2)[C@]([H])(O)[C@]1([H])O)P(O)(O)=O

InChI Identifier

InChI=1S/C9H16N5O8P/c10-1-5(13-9(11)14-6(1)17)12-7-3(16)2(15)4(22-7)8(18)23(19,20)21/h2-4,7-8,15-16,18H,10H2,(H2,19,20,21)(H4,11,12,13,14,17)/t2-,3+,4-,7?,8?/m0/s1

InChI Key

CIEXRWBOBYOQGW-DOAYSINJSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Glycosylamines

Alternative Parents

Substituents

N-glycosyl compound
Pentose monosaccharide
Secondary aliphatic/aromatic amine
Pyrimidone
Aminopyrimidine
Pyrimidine
Monosaccharide
Hydropyrimidine
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Organophosphonic acid derivative
Organophosphonic acid
Secondary alcohol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Secondary amine
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organophosphorus compound
Organonitrogen compound
Amine
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	6.36 g/L	ALOGPS
logP	-2.6	ALOGPS
logP	-4.4	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.25	ChemAxon
pKa (Strongest Basic)	21.89	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	233.97 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	92.41 m³·mol⁻¹	ChemAxon
Polarizability	30.01 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine

METLIN ID

Not Available

PubChem Compound

69612071

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine (MMDBc0029772)

MOL for #<Metabolite:0x00007f124136d440>

3D MOL for #<Metabolite:0x00007f124136d440>

3D SDF for #<Metabolite:0x00007f124136d440>

3D-SDF for #<Metabolite:0x00007f124136d440>

PDB for #<Metabolite:0x00007f124136d440>

3D PDB for #<Metabolite:0x00007f124136d440>

SMILES for #<Metabolite:0x00007f124136d440>

INCHI for #<Metabolite:0x00007f124136d440>

Structure for #<Metabolite:0x00007f124136d440>

3D Structure for #<Metabolite:0x00007f124136d440>