MiMeDB: Showing metabocard for 2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine (MMDBc0055225)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:46:48 UTC

Update Date

2022-08-12 20:09:17 UTC

Metabolite ID

MMDBc0055225

Metabolite Identification

Common Name

2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine

Description

2-(formamido)-N1-(5-phospho-beta-D-ribosyl)acetamidine 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. Based on a literature review very few articles have been published on 2-(formamido)-N1-(5-phospho-beta-D-ribosyl)acetamidine.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221462D          

 24 24  0  0  1  0            999 V2000
   -1.6351   -1.4039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7911   -0.5640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1501   -0.7365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4857    0.0172    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4555   -1.3177    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6116   -0.4778    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2022    0.8421    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6725   -0.1974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1626    1.3718    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6329    0.3323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4175    0.5872    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.3643    1.4442    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1673    1.4888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6830    0.0460    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5298   -0.8903    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  1  1  0  0  0
  5  1  1  0  0  0  0
  6  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  5  2  0  0  0  0
 10  1  1  0  0  0  0
 10  3  2  0  0  0  0
 11  5  1  0  0  0  0
  8 11  1  1  0  0  0
  3 12  1  4  0  0  0
  6 13  1  6  0  0  0
  7 14  1  6  0  0  0
 18  2  1  0  0  0  0
 19  4  1  0  0  0  0
 19  8  1  0  0  0  0
 20 15  1  0  0  0  0
 20 16  1  0  0  0  0
 20 17  2  0  0  0  0
 20 18  1  0  0  0  0
  4 21  1  6  0  0  0
  6 22  1  1  0  0  0
  7 23  1  1  0  0  0
  8 24  1  6  0  0  0
M  CHG  1  12  -1
M  END
> <DATABASE_ID>
MMDBc0055225

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(O)[C@@]([H])(O)[C@]([H])(NC(=N)CN=C[O-])O[C@]1([H])COP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H16N3O8P/c9-5(1-10-3-12)11-8-7(14)6(13)4(19-8)2-18-20(15,16)17/h3-4,6-8,13-14H,1-2H2,(H2,9,11)(H,10,12)(H2,15,16,17)/p-1/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
PMCOGCVKOAOZQM-XVFCMESISA-M

> <FORMULA>
C8H15N3O8P

> <MOLECULAR_WEIGHT>
312.195

> <EXACT_MASS>
312.060225033

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
26.146948576372512

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-({N-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]carbamimidoyl}methyl)carboximidate

> <JCHEM_LOGP>
-3.811329961264807

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.4014315821599093

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0707203020350677

> <JCHEM_PKA_STRONGEST_BASIC>
6.917527624102581

> <JCHEM_POLAR_SURFACE_AREA>
187.74999999999997

> <JCHEM_REFRACTIVITY>
83.7921

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
N-({N-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]carbamimidoyl}methyl)carboximidate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      -3.052  -2.621   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.770   1.651   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.210  -1.053   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.147  -1.375   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -2.773   0.032   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0      -4.584  -2.460   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0      -0.615  -1.536   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0      -6.742  -0.892   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       7.844   1.572   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       6.855  -0.369   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       5.904   2.561   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       4.915   0.620   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
HETATM   20  P   UNK     0       6.379   1.096   0.000  0.00  0.00           P+0
HETATM   21  H   UNK     0       2.547   2.696   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0      -0.312   2.779   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0      -1.275   0.086   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.989  -1.662   0.000  0.00  0.00           H+0
CONECT    1    5   10                                                       
CONECT    2    4   18                                                       
CONECT    3   10   12                                                       
CONECT    4    2    6   19   21                                             
CONECT    5    1    9   11                                                  
CONECT    6    4    7   13   22                                             
CONECT    7    6    8   14   23                                             
CONECT    8    7   11   19   24                                             
CONECT    9    5                                                            
CONECT   10    1    3                                                       
CONECT   11    5    8                                                       
CONECT   12    3                                                            
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15   20                                                            
CONECT   16   20                                                            
CONECT   17   20                                                            
CONECT   18    2   20                                                       
CONECT   19    4    8                                                       
CONECT   20   15   16   17   18                                             
CONECT   21    4                                                            
CONECT   22    6                                                            
CONECT   23    7                                                            
CONECT   24    8                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   48    0
END

Synonyms

Value	Source
2-(Formamido)-N1-(5-phospho-b-D-ribosyl)acetamidine	Generator
2-(Formamido)-N1-(5-phospho-β-D-ribosyl)acetamidine	Generator

Molecular Formula

C₈H₁₅N₃O₈P

Average Mass

312.195

Monoisotopic Mass

312.060225033

IUPAC Name

N-({N-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]carbamimidoyl}methyl)carboximidate

Traditional Name

N-({N-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]carbamimidoyl}methyl)carboximidate

CAS Registry Number

Not Available

SMILES

[H][C@]1(O)[C@@]([H])(O)[C@]([H])(NC(=N)CN=C[O-])O[C@]1([H])COP(O)(O)=O

InChI Identifier

InChI=1S/C8H16N3O8P/c9-5(1-10-3-12)11-8-7(14)6(13)4(19-8)2-18-20(15,16)17/h3-4,6-8,13-14H,1-2H2,(H2,9,11)(H,10,12)(H2,15,16,17)/p-1/t4-,6-,7-,8-/m1/s1

InChI Key

PMCOGCVKOAOZQM-XVFCMESISA-M

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
Organic phosphoric acid derivative
Alkyl phosphate
Phosphoric acid ester
Oxolane
1,2-diol
Carboxamide group
Secondary carboxylic acid amide
Secondary alcohol
Amidine
Carboxylic acid amidine
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Carboximidamide
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Carbonyl group
Organic salt
Organonitrogen compound
Alcohol
Organic cation
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
logP	-3.8	ChemAxon
pKa (Strongest Acidic)	1.07	ChemAxon
pKa (Strongest Basic)	6.92	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	187.75 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	83.79 m³·mol⁻¹	ChemAxon
Polarizability	26.15 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

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
MMDBr0014282	2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine	5-Aminoimidazole ribonucleotide	Bifunctional purine biosynthetic protein ADE5,7	Ligation	RHEA	34755880
MMDBr0017879	Adenosine triphosphate	2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine	Phosphoribosylformylglycinamidine synthase	Synthesis	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	Hosts and Body Sites
Eukaryota/Fungi	Basidiomycota	1
Eukaryota/Fungi	Ascomycota	4
Bacteria	Firmicutes	142	Human ; Human feces; Catfish ; Cattle ; Human supragingival plaque
Bacteria	Proteobacteria	304	Human ; Human feces; Pig ; Cattle ; River trout ; Rat ; Turkey ; Sheep ; Chicken
Archaea/Archaea	Euryarchaeota	31
Bacteria	Actinobacteria	41	Human ; Human feces; Cattle
Bacteria	Cyanobacteria	34	Human
Bacteria/NULL	Proteobacteria	2	Human ; Human feces; Pig ; Cattle ; River trout ; Rat ; Turkey ; Sheep ; Chicken
Bacteria	Fusobacteria	1	Human ; Human feces
Bacteria	Spirochaetes	7	Human
Archaea	Euryarchaeota	2
Bacteria	Thermotogae	3
Bacteria	Planctomycetes	1
Archaea	Crenarchaeota	1
Archaea/Archaea	Crenarchaeota	16
Bacteria	nah	1
Bacteria	Nitrospirae	1
Bacteria	Aquificae	1
Bacteria	Chlorobi	4
Bacteria	Deinococcus-thermus	4
Bacteria	Bacteroidetes	1
Bacteria	Chloroflexi	2
Bacteria	Acidobacteria	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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

90657386

PDB ID

Not Available

ChEBI ID

Not Available

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-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine (MMDBc0055225)

MOL for #<Metabolite:0x00007f5a7c03dee0>

3D MOL for #<Metabolite:0x00007f5a7c03dee0>

3D SDF for #<Metabolite:0x00007f5a7c03dee0>

3D-SDF for #<Metabolite:0x00007f5a7c03dee0>

PDB for #<Metabolite:0x00007f5a7c03dee0>

3D PDB for #<Metabolite:0x00007f5a7c03dee0>

SMILES for #<Metabolite:0x00007f5a7c03dee0>

INCHI for #<Metabolite:0x00007f5a7c03dee0>

Structure for #<Metabolite:0x00007f5a7c03dee0>

3D Structure for #<Metabolite:0x00007f5a7c03dee0>