MiMeDB: Showing metabocard for 2-amino-5-formylamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one (MMDBc0054159)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 22:56:30 UTC

Update Date

2022-09-01 02:27:34 UTC

Metabolite ID

MMDBc0054159

Metabolite Identification

Common Name

2-amino-5-formylamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one

Description

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006051502262D          
 
 25 26  0  0  1  0            999 V2000
   17.3220  -12.1817    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.9507  -12.6262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5544  -12.4352    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.6835  -12.0810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.0305  -13.4703    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.8771  -11.9247    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.2975  -13.1785    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.4612  -11.3585    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.4267  -12.4143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8189  -13.8141    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2207  -12.4005    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.4778  -13.1785    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.7767  -13.8488    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.5239  -13.2966    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.0832  -11.9211    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.9093  -14.6372    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.4358  -12.1400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2104  -13.9600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8177  -12.6923    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.9876  -12.6923    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   12.1540  -12.6923    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.9806  -13.5223    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.9806  -11.8621    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.9624  -10.6827    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.7931  -10.7782    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  1  1  1  0  0  0
  2  4  2  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  9  1  0  0  0  0
  5 10  2  0  0  0  0
  6 11  1  0  0  0  0
  7 12  1  0  0  0  0
  7 13  1  6  0  0  0
  9 14  1  0  0  0  0
  9 15  2  0  0  0  0
 10 16  1  0  0  0  0
 11 17  1  1  0  0  0
 12 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 20 23  2  0  0  0  0
  4  8  1  0  0  0  0
 10 14  1  0  0  0  0
 11 12  1  0  0  0  0
  8 24  1  0  0  0  0
 24 25  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054159

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=NC(N[C@@H]2O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]2O)=C(NC=O)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C10H16N5O9P/c11-10-14-7(4(12-2-16)8(19)15-10)13-9-6(18)5(17)3(24-9)1-23-25(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,12,16)(H2,20,21,22)(H4,11,13,14,15,19)/t3-,5-,6-,9-/m1/s1

> <INCHI_KEY>
VKMYTDDVUBGBDH-UUOKFMHZSA-N

> <FORMULA>
C10H16N5O9P

> <MOLECULAR_WEIGHT>
381.238

> <EXACT_MASS>
381.068564113

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
31.48958230308574

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-5-[(2-amino-5-formamido-6-oxo-1,6-dihydropyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-2.08

> <JCHEM_LOGP>
-4.230863104102144

> <ALOGPS_LOGS>
-1.95

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.239234787142979

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.368265565647829

> <JCHEM_PKA_STRONGEST_BASIC>
0.6727916985489327

> <JCHEM_POLAR_SURFACE_AREA>
225.05999999999997

> <JCHEM_REFRACTIVITY>
87.00979999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.32e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-5-[(2-amino-5-formamido-6-oxo-1H-pyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl]methoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-JUN-15         0                                  
HETATM    1  N   UNK     0      32.334 -22.739   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      33.508 -23.569   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      30.902 -23.212   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      34.876 -22.551   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      33.657 -25.145   0.000  0.00  0.00           N+0
HETATM    6  O   UNK     0      29.637 -22.259   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      30.422 -24.600   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      34.461 -21.203   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      36.263 -23.173   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      35.129 -25.786   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      28.412 -23.148   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      28.892 -24.600   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      31.316 -25.851   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0      36.445 -24.820   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0      37.489 -22.253   0.000  0.00  0.00           O+0
HETATM   16  N   UNK     0      35.297 -27.323   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      26.947 -22.661   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      28.393 -26.059   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      25.793 -23.692   0.000  0.00  0.00           O+0
HETATM   20  P   UNK     0      24.243 -23.692   0.000  0.00  0.00           P+0
HETATM   21  O   UNK     0      22.687 -23.692   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      24.231 -25.242   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      24.231 -22.143   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      35.397 -19.941   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      36.947 -20.119   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4    5                                                  
CONECT    3    1    6    7                                                  
CONECT    4    2    9    8                                                  
CONECT    5    2   10                                                       
CONECT    6    3   11                                                       
CONECT    7    3   12   13                                                  
CONECT    8    4   24                                                       
CONECT    9    4   14   15                                                  
CONECT   10    5   16   14                                                  
CONECT   11    6   17   12                                                  
CONECT   12    7   18   11                                                  
CONECT   13    7                                                            
CONECT   14    9   10                                                       
CONECT   15    9                                                            
CONECT   16   10                                                            
CONECT   17   11   19                                                       
CONECT   18   12                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21   22   23                                             
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   20                                                            
CONECT   24    8   25                                                       
CONECT   25   24                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   52    0
END

Synonyms

Value	Source
2-Amino-5-formylamino-6-(1-D-ribosylamino)-4(3H)-pyrimidinone 5'-monophosphate	ChEBI
2-Amino-5-formylamino-6-(1-D-ribosylamino)-4(3H)-pyrimidinone 5'-phosphate	ChEBI
2-Amino-5-formylamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-monophosphate	ChEBI
2-Amino-5-formylamino-6-(5-phosphoribosylamino)pyrimidin-4(3H)-one	ChEBI
2-Amino-5-formylamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine	ChEBI
2-Amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-monophosphate	ChEBI
2-Amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate	ChEBI
2-Amino-5-formylamino-6-(1-D-ribosylamino)-4(3H)-pyrimidinone 5'-monophosphoric acid	Generator
2-Amino-5-formylamino-6-(1-D-ribosylamino)-4(3H)-pyrimidinone 5'-phosphoric acid	Generator
2-Amino-5-formylamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-monophosphoric acid	Generator
2-Amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-monophosphoric acid	Generator
2-Amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphoric acid	Generator
2-Amino-5-formylamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphoric acid	Generator

Molecular Formula

C₁₀H₁₆N₅O₉P

Average Mass

381.238

Monoisotopic Mass

381.068564113

IUPAC Name

{[(2R,3S,4R,5R)-5-[(2-amino-5-formamido-6-oxo-1,6-dihydropyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional Name

[(2R,3S,4R,5R)-5-[(2-amino-5-formamido-6-oxo-1H-pyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl]methoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

NC1=NC(N[C@@H]2O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]2O)=C(NC=O)C(=O)N1

InChI Identifier

InChI=1S/C10H16N5O9P/c11-10-14-7(4(12-2-16)8(19)15-10)13-9-6(18)5(17)3(24-9)1-23-25(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,12,16)(H2,20,21,22)(H4,11,13,14,15,19)/t3-,5-,6-,9-/m1/s1

InChI Key

VKMYTDDVUBGBDH-UUOKFMHZSA-N

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
N-arylamide
Aminopyrimidine
Pyrimidone
Secondary aliphatic/aromatic amine
Monoalkyl phosphate
Alkyl phosphate
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Vinylogous amide
Tetrahydrofuran
Heteroaromatic compound
Amino acid or derivatives
1,2-diol
Carboxamide group
Secondary carboxylic acid amide
Secondary alcohol
Secondary amine
Azacycle
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Carbonyl group
Hydrocarbon derivative
Amine
Primary amine
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

aminopyrimidine (CHEBI:11515 )
pyrimidone (CHEBI:11515 )
N-glycosyl compound (CHEBI:11515 )
ribose monophosphate (CHEBI:11515 )
formamidopyrimidine (CHEBI:11515 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	4.32 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-4.2	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	1.37	ChemAxon
pKa (Strongest Basic)	0.67	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	225.06 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	87.01 m³·mol⁻¹	ChemAxon
Polarizability	31.49 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 GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_6_44) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00ec-0915000000-4b635f01d86b41b8873f	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-006x-1900000000-6074bcccc349bff613c5	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0h93-2900000000-f297efacca5fc65673c6	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00lr-3925000000-5338ccd774f1e95892b5	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9301000000-c7878352cd904c0c4619	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-2089d70a794c63841d45	2019-02-23	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0014214	Guanosine triphosphate	2-amino-5-formylamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one	GTP cyclohydrolase III	Hydrolysis	RHEA	34755880
MMDBr0014662	2-amino-5-formylamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one	2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine	2-amino-5-formylamino-6-ribosylaminopyrimidin-4(3H)-one 5'-monophosphate deformylase	Removal of the N-terminal formyl group	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
Archaea/Archaea	Crenarchaeota	13
Archaea/Archaea	Euryarchaeota	18
Archaea	Euryarchaeota	3
Archaea	Crenarchaeota	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

Not Available

KEGG Compound ID

C15563

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5460646

PDB ID

Not Available

ChEBI ID

11515

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 2-amino-5-formylamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one (MMDBc0054159)

MOL for #<Metabolite:0x00007f5a84013548>

3D MOL for #<Metabolite:0x00007f5a84013548>

3D SDF for #<Metabolite:0x00007f5a84013548>

3D-SDF for #<Metabolite:0x00007f5a84013548>

PDB for #<Metabolite:0x00007f5a84013548>

3D PDB for #<Metabolite:0x00007f5a84013548>

SMILES for #<Metabolite:0x00007f5a84013548>

INCHI for #<Metabolite:0x00007f5a84013548>

Structure for #<Metabolite:0x00007f5a84013548>

3D Structure for #<Metabolite:0x00007f5a84013548>