MiMeDB: Showing metabocard for 2-(Formamido)-N1-(5-phospho-D-ribosyl)acetamidine (MMDBc0032017)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:58:47 UTC

Update Date

2022-08-31 18:27:32 UTC

Metabolite ID

MMDBc0032017

Metabolite Identification

Common Name

2-(Formamido)-N1-(5-phospho-D-ribosyl)acetamidine

Description

NULL

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231220332D          

 18 18  0  0  1  0            999 V2000
   19.1661  -12.5824    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9198  -12.2468    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.4958  -14.7759    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   19.9808  -15.4434    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.4958  -16.1108    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.7112  -15.8559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7112  -15.0309    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   18.0437  -14.5460    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.1300  -13.7255    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4625  -13.2406    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.8836  -13.3899    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.7507  -13.9913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.8058  -15.4434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.7507  -16.8954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.6467  -18.1217    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.5856  -16.9565    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.8118  -18.0606    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.1987  -17.5085    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  7  3  1  0  0  0  0
  7  8  1  1  0  0  0
  9  8  1  0  0  0  0
 10  9  2  0  0  0  0
 11  9  1  0  0  0  0
  1 11  1  0  0  0  0
  3 12  1  6  0  0  0
  4 13  1  6  0  0  0
  5 14  1  1  0  0  0
 17 18  1  0  0  0  0
 16 18  2  0  0  0  0
 15 18  1  0  0  0  0
 14 18  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0032017

> <DATABASE_NAME>
MIME

> <SMILES>
O[C@@H]1[C@H](O)[C@@H](OP(O)(O)=O)O[C@H]1NC(=N)NC=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12N3O8P/c7-6(8-1-10)9-4-2(11)3(12)5(16-4)17-18(13,14)15/h1-5,11-12H,(H2,13,14,15)(H3,7,8,9,10)/t2-,3+,4-,5-/m1/s1

> <INCHI_KEY>
OKXISSDNJVDCJE-KKQCNMDGSA-N

> <FORMULA>
C6H12N3O8P

> <MOLECULAR_WEIGHT>
285.1485

> <EXACT_MASS>
285.036200887

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
22.68962556497434

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-3,4-dihydroxy-5-[(formamidomethanimidoyl)amino]oxolan-2-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-2.07

> <JCHEM_LOGP>
-3.117339851729372

> <ALOGPS_LOGS>
-1.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.265948157804224

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.118556859786445

> <JCHEM_PKA_STRONGEST_BASIC>
5.258678507329495

> <JCHEM_POLAR_SURFACE_AREA>
181.42999999999998

> <JCHEM_REFRACTIVITY>
63.2266

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.66e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-3,4-dihydroxy-5-[(formamidomethanimidoyl)amino]oxolan-2-yl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      35.777 -23.487   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      37.184 -22.861   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      36.392 -27.582   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      37.297 -28.828   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      36.392 -30.073   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      34.928 -29.598   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      34.928 -28.058   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      33.682 -27.153   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      33.843 -25.621   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      32.597 -24.716   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0      35.249 -24.994   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0      36.868 -26.117   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      38.837 -28.828   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      36.868 -31.538   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      34.807 -33.827   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      34.693 -31.652   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      36.982 -33.713   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0      35.838 -32.683   0.000  0.00  0.00           P+0
CONECT    1    2   11                                                       
CONECT    2    1                                                            
CONECT    3    4    7   12                                                  
CONECT    4    3    5   13                                                  
CONECT    5    4    6   14                                                  
CONECT    6    5    7                                                       
CONECT    7    6    3    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    1                                                       
CONECT   12    3                                                            
CONECT   13    4                                                            
CONECT   14    5   18                                                       
CONECT   15   18                                                            
CONECT   16   18                                                            
CONECT   17   18                                                            
CONECT   18   17   16   15   14                                             
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

Synonyms

Value	Source
1-(5'-Phosphoribosyl)-N-formylglycinamidine	HMDB
1-Deoxy-1-[2-(formamido)acetimidamido]-D-ribofuranose 5-(dihydrogen phosphate)	HMDB
2-(Formamido)-N(1)-(5'-phosphoribosyl)acetamidine	HMDB
2-(Formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine	HMDB
2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine	HMDB
5'-Phosphoribosyl-N-formylglycinamidine	HMDB
5'-Phosphoribosylformylglycinamidine	HMDB
FGAM	HMDB
N-[2-(Formamido)ethanimidoyl]-5-O-phosphono-D-ribofuranosylamine	HMDB
[(2R,3S,4R,5R)-5-[(1-Amino-2-formamido-ethylidene)amino]-3,4-dihydroxy-oxolan-2-yl]methoxyphosphonic acid	HMDB

Molecular Formula

C₆H₁₂N₃O₈P

Average Mass

285.1485

Monoisotopic Mass

285.036200887

IUPAC Name

{[(2R,3S,4R,5R)-3,4-dihydroxy-5-[(formamidomethanimidoyl)amino]oxolan-2-yl]oxy}phosphonic acid

Traditional Name

[(2R,3S,4R,5R)-3,4-dihydroxy-5-[(formamidomethanimidoyl)amino]oxolan-2-yl]oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

O[C@@H]1[C@H](O)[C@@H](OP(O)(O)=O)O[C@H]1NC(=N)NC=O

InChI Identifier

InChI=1S/C6H12N3O8P/c7-6(8-1-10)9-4-2(11)3(12)5(16-4)17-18(13,14)15/h1-5,11-12H,(H2,13,14,15)(H3,7,8,9,10)/t2-,3+,4-,5-/m1/s1

InChI Key

OKXISSDNJVDCJE-KKQCNMDGSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Monoalkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Tetrahydrofuran
1,2-diol
Guanidine
Secondary alcohol
Oxacycle
Carboximidamide
Carboxylic acid derivative
Organoheterocyclic compound
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organonitrogen compound
Organic nitrogen compound
Alcohol
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	7.66 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-3.1	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.12	ChemAxon
pKa (Strongest Basic)	5.26	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	181.43 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	63.23 m³·mol⁻¹	ChemAxon
Polarizability	22.69 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	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

Cytoplasm

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
MMDBr0018508	L-Glutamine	L-Glutamic acid	Phosphoribosylformylglycinamidine synthase	Synthesis	PathBank	31602464
MMDBr0018509	2-(Formamido)-N1-(5-phospho-D-ribosyl)acetamidine	5-Aminoimidazole ribonucleotide	Phosphoribosylformylglycinamidine cyclo-ligase	Ligation	PathBank	31602464
MMDBr0019838	L-Glutamine	L-Glutamic acid	Unknown Protein		PathBank	31602464
MMDBr0019839	2-(Formamido)-N1-(5-phospho-D-ribosyl)acetamidine	5-Aminoimidazole ribonucleotide	Unknown Protein		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
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
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

HMDB0006211

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023837

KNApSAcK ID

Not Available

Chemspider ID

17216355

KEGG Compound ID

C04640

BioCyc ID

5-PHOSPHORIBOSYL-N-FORMYLGLYCINEAMIDINE

BiGG ID

44236

Wikipedia Link

Not Available

METLIN ID

3442

PubChem Compound

22833657

PDB ID

Not Available

ChEBI ID

18413

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-(Formamido)-N1-(5-phospho-D-ribosyl)acetamidine (MMDBc0032017)

MOL for #<Metabolite:0x00007f9208027000>

3D MOL for #<Metabolite:0x00007f9208027000>

3D SDF for #<Metabolite:0x00007f9208027000>

3D-SDF for #<Metabolite:0x00007f9208027000>

PDB for #<Metabolite:0x00007f9208027000>

3D PDB for #<Metabolite:0x00007f9208027000>

SMILES for #<Metabolite:0x00007f9208027000>

INCHI for #<Metabolite:0x00007f9208027000>

Structure for #<Metabolite:0x00007f9208027000>

3D Structure for #<Metabolite:0x00007f9208027000>