MiMeDB: Showing metabocard for 2,5-Diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate (MMDBc0047872)

Microbial

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-11-19 15:46:56 UTC

Update Date

2025-10-07 16:08:08 UTC

Metabolite ID

MMDBc0047872

Metabolite Identification

Common Name

2,5-Diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate

Description

2,5-Diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate is a pyrimidine derivative and belongs to the class of nucleotides. There is limited literature available on this metabolite, indicating that further research may be needed to fully understand its biological significance and functions.

Structure

MOL SDF PDB SMILES InChI


  Mrv1572001051620392D          

 23 23  0  0  0  0            999 V2000
   -1.9419    1.3830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6564    0.9705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6564    0.1454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9419   -0.2669    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2274    0.1454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2274    0.9705    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9419    2.2080    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3709    1.3830    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3709   -0.2671    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5130   -0.2671    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3708   -1.0921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6563   -1.5045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6563   -2.3295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9419   -1.0920    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -3.3707   -2.7421    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.9418   -2.7420    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9417   -3.5670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2273   -2.3294    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.2272   -3.9794    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0537   -4.0136    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0448   -4.8163    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0798   -3.1584    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7709   -4.0376    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  0  0  0  0
 12 14  1  0  0  0  0
 16 18  1  0  0  0  0
 13 15  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 23  1  0  0  0  0
 20 22  1  0  0  0  0
  3  9  1  0  0  0  0
  9 11  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5 10  1  0  0  0  0
  1  6  1  0  0  0  0
  5  6  1  0  0  0  0
  2  8  1  0  0  0  0
  1  7  2  0  0  0  0
M  CHG  5  14  -1  15  -1  18  -1  22  -1  23  -1
M  END
> <DATABASE_ID>
MMDBc0047872

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=NC(NCC([O-])C([O-])C([O-])COP([O-])([O-])=O)=C(N)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C9H15N5O8P/c10-5-7(13-9(11)14-8(5)18)12-1-3(15)6(17)4(16)2-22-23(19,20)21/h3-4,6H,1-2,10H2,(H2,19,20,21)(H4,11,12,13,14,18)/q-3/p-2

> <INCHI_KEY>
YZXAOFZAYKDDIC-UHFFFAOYSA-L

> <FORMULA>
C9H13N5O8P

> <MOLECULAR_WEIGHT>
350.207

> <EXACT_MASS>
350.052917296

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
29.758753792686225

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-5

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2,5-diamino-6-oxo-1,6-dihydropyrimidin-4-yl)amino]-5-(phosphonatooxy)pentane-2,3,4-tris(olate)

> <ALOGPS_LOGP>
-1.37

> <JCHEM_LOGP>
-5.023263190622112

> <ALOGPS_LOGS>
-1.67

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
1.8942484435927591

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2730330528048808

> <JCHEM_PKA_STRONGEST_BASIC>
6.497186814325184

> <JCHEM_POLAR_SURFACE_AREA>
247.13

> <JCHEM_REFRACTIVITY>
113.94419999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.28e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2,5-diamino-6-oxo-1H-pyrimidin-4-yl)amino]-5-(phosphonatooxy)pentane-2,3,4-tris(olate)

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-JAN-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-JAN-16         0                                  
HETATM    1  C   UNK     0      -3.625   2.582   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.959   1.812   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.959   0.271   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -3.625  -0.498   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -2.291   0.271   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -2.291   1.812   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0      -3.625   4.122   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0      -6.292   2.582   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0      -6.292  -0.499   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0      -0.958  -0.499   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -6.292  -2.039   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -4.958  -2.808   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.958  -4.348   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -3.625  -2.038   0.000  0.00  0.00           O-1
HETATM   15  O   UNK     0      -6.292  -5.119   0.000  0.00  0.00           O-1
HETATM   16  C   UNK     0      -3.625  -5.118   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -3.625  -6.658   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.291  -4.348   0.000  0.00  0.00           O-1
HETATM   19  O   UNK     0      -2.291  -7.428   0.000  0.00  0.00           O+0
HETATM   20  P   UNK     0      -0.100  -7.492   0.000  0.00  0.00           P+0
HETATM   21  O   UNK     0      -0.084  -8.990   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -0.149  -5.896   0.000  0.00  0.00           O-1
HETATM   23  O   UNK     0       1.439  -7.537   0.000  0.00  0.00           O-1
CONECT    1    2    6    7                                                  
CONECT    2    1    3    8                                                  
CONECT    3    2    9    4                                                  
CONECT    4    3    5                                                       
CONECT    5    4   10    6                                                  
CONECT    6    1    5                                                       
CONECT    7    1                                                            
CONECT    8    2                                                            
CONECT    9    3   11                                                       
CONECT   10    5                                                            
CONECT   11   12    9                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12   16   15                                                  
CONECT   14   12                                                            
CONECT   15   13                                                            
CONECT   16   13   17   18                                                  
CONECT   17   16   19                                                       
CONECT   18   16                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21   23   22                                             
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   20                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

Synonyms

Value	Source
2,5-Diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphoric acid	Generator

Molecular Formula

C₉H₁₃N₅O₈P

Average Mass

350.207

Monoisotopic Mass

350.052917296

IUPAC Name

1-[(2,5-diamino-6-oxo-1,6-dihydropyrimidin-4-yl)amino]-5-(phosphonatooxy)pentane-2,3,4-tris(olate)

Traditional Name

1-[(2,5-diamino-6-oxo-1H-pyrimidin-4-yl)amino]-5-(phosphonatooxy)pentane-2,3,4-tris(olate)

CAS Registry Number

Not Available

SMILES

NC1=NC(NCC([O-])C([O-])C([O-])COP([O-])([O-])=O)=C(N)C(=O)N1

InChI Identifier

InChI=1S/C9H15N5O8P/c10-5-7(13-9(11)14-8(5)18)12-1-3(15)6(17)4(16)2-22-23(19,20)21/h3-4,6H,1-2,10H2,(H2,19,20,21)(H4,11,12,13,14,18)/q-3/p-2

InChI Key

YZXAOFZAYKDDIC-UHFFFAOYSA-L

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
Secondary aliphatic/aromatic amine
Aminopyrimidine
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
Hydropyrimidine
Heteroaromatic compound
Azacycle
Organoheterocyclic compound
Secondary amine
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Alkoxide
Primary amine
Organonitrogen compound
Amine
Organic anion
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	9.28 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-5	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.27	ChemAxon
pKa (Strongest Basic)	6.5	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	247.13 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	113.94 m³·mol⁻¹	ChemAxon
Polarizability	29.76 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-1109000000-4061578754a0b15ff39e	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-4219000000-6fc37ed856b6e969cf4d	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01ot-9532000000-b4ab91e39909cd9c5621	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-1009000000-4f793393a9377cb10e65	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001j-9001000000-55e76e7e7551863da52d	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-003s-9000000000-6e0a00c301e03c79c0c8	2016-09-14	View Spectrum

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

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank	Species

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
MMDBr0019644	2,5-Diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate	2,5-Diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate	2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase	Reduction	PathBank	31602464
MMDBr0019645	2,5-Diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate	5-Amino-2,6-dioxy-4-(5'-phospho-D-ribitylamino)pyrimidine	Bifunctional protein RIB2	Synthesis	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
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

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

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 2,5-Diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate (MMDBc0047872)

MOL for #<Metabolite:0x00007f2ac8160590>

3D MOL for #<Metabolite:0x00007f2ac8160590>

3D SDF for #<Metabolite:0x00007f2ac8160590>

3D-SDF for #<Metabolite:0x00007f2ac8160590>

PDB for #<Metabolite:0x00007f2ac8160590>

3D PDB for #<Metabolite:0x00007f2ac8160590>

SMILES for #<Metabolite:0x00007f2ac8160590>

INCHI for #<Metabolite:0x00007f2ac8160590>

Structure for #<Metabolite:0x00007f2ac8160590>

3D Structure for #<Metabolite:0x00007f2ac8160590>