MiMeDB: Showing metabocard for 2,5-Diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate (MMDBc0047871)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 15:46:52 UTC

Update Date

2022-09-01 02:00:28 UTC

Metabolite ID

MMDBc0047871

Metabolite Identification

Common Name

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

Description

Structure

MOL SDF PDB SMILES InChI


  Mrv1572001051620022D          

 23 24  0  0  0  0            999 V2000
    1.9196    2.3428    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2051    1.9303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2051    1.1052    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9196    0.6928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6341    1.1052    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6341    1.9303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4906    2.3428    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3486    2.3428    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4906    0.6927    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9196   -0.1321    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2051   -0.5446    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4514   -0.2091    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1005   -0.8222    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3119   -1.5366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1188   -1.3651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0236   -2.2903    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.8152   -1.9722    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.9210   -0.7359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7449   -0.6927    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7969   -0.7150    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8395    0.1094    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.7572   -1.5840    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7811   -0.7135    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  6  8  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  3  9  1  0  0  0  0
  4 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 15  1  0  0  0  0
  2  7  2  0  0  0  0
 12 13  1  0  0  0  0
 11 12  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 13 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 22  2  0  0  0  0
 20 23  1  0  0  0  0
 20 21  1  0  0  0  0
 15 17  1  0  0  0  0
 14 16  1  0  0  0  0
M  CHG  4  16  -1  17  -1  21  -1  23  -1
M  END
> <DATABASE_ID>
MMDBc0047871

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=NC(NC2OC(COP([O-])([O-])=O)C([O-])C2[O-])=C(N)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N5O8P/c10-3-6(13-9(11)14-7(3)17)12-8-5(16)4(15)2(22-8)1-21-23(18,19)20/h2,4-5,8H,1,10H2,(H2,18,19,20)(H4,11,12,13,14,17)/q-2/p-2

> <INCHI_KEY>
MIOOSFCUZYDRQJ-UHFFFAOYSA-L

> <FORMULA>
C9H12N5O8P

> <MOLECULAR_WEIGHT>
349.198

> <EXACT_MASS>
349.044543684

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
28.362874934127152

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-4

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.52

> <JCHEM_LOGP>
-4.229215585172958

> <ALOGPS_LOGS>
-1.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.240036904553057

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.05277451592268

> <JCHEM_PKA_STRONGEST_BASIC>
1.7093613607160465

> <JCHEM_POLAR_SURFACE_AREA>
233.29999999999998

> <JCHEM_REFRACTIVITY>
100.91369999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.63e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[(2,5-diamino-6-oxo-1H-pyrimidin-4-yl)amino]-5-[(phosphonatooxy)methyl]oxolane-3,4-bis(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  N   UNK     0       3.583   4.373   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       2.250   3.603   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.250   2.063   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.583   1.293   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       4.917   2.063   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       4.917   3.603   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.916   4.373   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       6.251   4.373   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       0.916   1.293   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       3.583  -0.247   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       2.250  -1.017   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.843  -0.390   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.188  -1.535   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.582  -2.868   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.088  -2.548   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -0.044  -4.275   0.000  0.00  0.00           O-1
HETATM   17  O   UNK     0       3.388  -3.681   0.000  0.00  0.00           O-1
HETATM   18  C   UNK     0      -1.719  -1.374   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -3.257  -1.293   0.000  0.00  0.00           O+0
HETATM   20  P   UNK     0      -5.221  -1.335   0.000  0.00  0.00           P+0
HETATM   21  O   UNK     0      -5.300   0.204   0.000  0.00  0.00           O-1
HETATM   22  O   UNK     0      -5.147  -2.957   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -7.058  -1.332   0.000  0.00  0.00           O-1
CONECT    1    2    6                                                       
CONECT    2    3    1    7                                                  
CONECT    3    2    4    9                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6                                                       
CONECT    6    1    8    5                                                  
CONECT    7    2                                                            
CONECT    8    6                                                            
CONECT    9    3                                                            
CONECT   10    4   11                                                       
CONECT   11   10   15   12                                                  
CONECT   12   13   11                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15   16                                                  
CONECT   15   11   14   17                                                  
CONECT   16   14                                                            
CONECT   17   15                                                            
CONECT   18   13   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   22   23   21                                             
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   20                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

Synonyms

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

Molecular Formula

C₉H₁₂N₅O₈P

Average Mass

349.198

Monoisotopic Mass

349.044543684

IUPAC Name

2-[(2,5-diamino-6-oxo-1,6-dihydropyrimidin-4-yl)amino]-5-[(phosphonatooxy)methyl]oxolane-3,4-bis(olate)

Traditional Name

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

CAS Registry Number

Not Available

SMILES

NC1=NC(NC2OC(COP([O-])([O-])=O)C([O-])C2[O-])=C(N)C(=O)N1

InChI Identifier

InChI=1S/C9H14N5O8P/c10-3-6(13-9(11)14-7(3)17)12-8-5(16)4(15)2(22-8)1-21-23(18,19)20/h2,4-5,8H,1,10H2,(H2,18,19,20)(H4,11,12,13,14,17)/q-2/p-2

InChI Key

MIOOSFCUZYDRQJ-UHFFFAOYSA-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-5-phosphate
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Monosaccharide phosphate
Secondary aliphatic/aromatic amine
Aminopyrimidine
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
Hydropyrimidine
Heteroaromatic compound
Tetrahydrofuran
Oxacycle
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	16.3 g/L	ALOGPS
logP	-1.5	ALOGPS
logP	-4.2	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	1.05	ChemAxon
pKa (Strongest Basic)	1.71	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	233.3 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	100.91 m³·mol⁻¹	ChemAxon
Polarizability	28.36 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0w29-2709000000-a66a3ccf9610baf28175	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0005-5019000000-d019a7ed52a291536d51	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03ed-9700000000-a3572b98ce61e5de3345	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-1009000000-067062858720dffd9af5	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001j-9001000000-ae904a0e438e78e15586	2016-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-003s-9000000000-e2fdc0af1da51cc70dbd	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

Metabolic Reactions

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
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

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

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

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-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate (MMDBc0047871)

MOL for #<Metabolite:0x00007fed153df018>

3D MOL for #<Metabolite:0x00007fed153df018>

3D SDF for #<Metabolite:0x00007fed153df018>

3D-SDF for #<Metabolite:0x00007fed153df018>

PDB for #<Metabolite:0x00007fed153df018>

3D PDB for #<Metabolite:0x00007fed153df018>

SMILES for #<Metabolite:0x00007fed153df018>

INCHI for #<Metabolite:0x00007fed153df018>

Structure for #<Metabolite:0x00007fed153df018>

3D Structure for #<Metabolite:0x00007fed153df018>