MiMeDB: Showing metabocard for 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole (MMDBc0031731)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:46:52 UTC

Update Date

2022-08-31 18:24:00 UTC

Metabolite ID

MMDBc0031731

Metabolite Identification

Common Name

5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole

Description

A 1-(phosphoribosyl)imidazole having the phospho group at the 5'-position and a carboxyamino group at the 5-position on the imidazole ring

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 10101211122D          

 26 27  0  0  0  0            999 V2000
    1.9239    2.7489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7605    4.4559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8439    1.9642    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2756    3.7884    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2564    3.2338    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5305    3.0038    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8631    2.5189    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1956    3.0038    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9709    4.4713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6689    1.9642    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2564    4.0588    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5890    2.7489    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3151    2.7489    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8631    1.6939    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9709    5.2963    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6854    4.0588    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3948    6.5444    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2424    6.3619    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5773    5.3921    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4249    5.2095    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4506    3.7884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9099    5.8770    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9971    3.3885    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2782    3.3525    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5982    2.1443    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0666    2.1890    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  1  1  0  0  0
  5  1  2  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
 10  1  1  0  0  0  0
 10  3  2  0  0  0  0
 11  5  1  0  0  0  0
 11  9  1  0  0  0  0
 12  3  1  0  0  0  0
 12  5  1  0  0  0  0
  8 12  1  1  0  0  0
  6 13  1  6  0  0  0
  7 14  1  6  0  0  0
 15  9  2  0  0  0  0
 16  9  1  0  0  0  0
 20  2  1  0  0  0  0
 21  4  1  0  0  0  0
 21  8  1  0  0  0  0
 22 17  1  0  0  0  0
 22 18  1  0  0  0  0
 22 19  2  0  0  0  0
 22 20  1  0  0  0  0
  4 23  1  6  0  0  0
  6 24  1  1  0  0  0
  7 25  1  1  0  0  0
  8 26  1  6  0  0  0
M  END


  Mrv0541 10101211122D          

 26 27  0  0  0  0            999 V2000
    1.9239    2.7489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7605    4.4559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8439    1.9642    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2756    3.7884    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2564    3.2338    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5305    3.0038    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8631    2.5189    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1956    3.0038    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9709    4.4713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6689    1.9642    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2564    4.0588    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5890    2.7489    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3151    2.7489    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8631    1.6939    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9709    5.2963    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6854    4.0588    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3948    6.5444    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2424    6.3619    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5773    5.3921    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4249    5.2095    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4506    3.7884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9099    5.8770    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9971    3.3885    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2782    3.3525    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5982    2.1443    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0666    2.1890    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  1  1  0  0  0
  5  1  2  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
 10  1  1  0  0  0  0
 10  3  2  0  0  0  0
 11  5  1  0  0  0  0
 11  9  1  0  0  0  0
 12  3  1  0  0  0  0
 12  5  1  0  0  0  0
  8 12  1  1  0  0  0
  6 13  1  6  0  0  0
  7 14  1  6  0  0  0
 15  9  2  0  0  0  0
 16  9  1  0  0  0  0
 20  2  1  0  0  0  0
 21  4  1  0  0  0  0
 21  8  1  0  0  0  0
 22 17  1  0  0  0  0
 22 18  1  0  0  0  0
 22 19  2  0  0  0  0
 22 20  1  0  0  0  0
  4 23  1  6  0  0  0
  6 24  1  1  0  0  0
  7 25  1  1  0  0  0
  8 26  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031731

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(COP(O)(O)=O)O[C@@]([H])(N2C=NC=C2NC(O)=O)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N3O9P/c13-6-4(2-20-22(17,18)19)21-8(7(6)14)12-3-10-1-5(12)11-9(15)16/h1,3-4,6-8,11,13-14H,2H2,(H,15,16)(H2,17,18,19)/t4-,6-,7-,8-/m1/s1

> <INCHI_KEY>
JHLXDWGVSYMXPL-XVFCMESISA-N

> <FORMULA>
C9H14N3O9P

> <MOLECULAR_WEIGHT>
339.1959

> <EXACT_MASS>
339.046765573

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
28.22678254830636

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-1H-imidazol-5-yl}carbamic acid

> <ALOGPS_LOGP>
-2.13

> <JCHEM_LOGP>
-3.4212731610733864

> <ALOGPS_LOGS>
-2.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.2551828758389445

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1822089997363596

> <JCHEM_PKA_STRONGEST_BASIC>
5.825351746342738

> <JCHEM_POLAR_SURFACE_AREA>
183.59999999999997

> <JCHEM_REFRACTIVITY>
67.4528

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.61e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]imidazol-4-ylcarbamic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-OCT-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   23  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    5   10                                                       
CONECT    2    4   20                                                       
CONECT    3   10   12                                                       
CONECT    4    2    6   21   23                                             
CONECT    5    1   11   12                                                  
CONECT    6    4    7   13   24                                             
CONECT    7    6    8   14   25                                             
CONECT    8    7   12   21   26                                             
CONECT    9   11   15   16                                                  
CONECT   10    1    3                                                       
CONECT   11    5    9                                                       
CONECT   12    3    5    8                                                  
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15    9                                                            
CONECT   16    9                                                            
CONECT   17   22                                                            
CONECT   18   22                                                            
CONECT   19   22                                                            
CONECT   20    2   22                                                       
CONECT   21    4    8                                                       
CONECT   22   17   18   19   20                                             
CONECT   23    4                                                            
CONECT   24    6                                                            
CONECT   25    7                                                            
CONECT   26    8                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   54    0
END

Synonyms

Not Available

Molecular Formula

C₉H₁₄N₃O₉P

Average Mass

339.1959

Monoisotopic Mass

339.046765573

IUPAC Name

{1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-1H-imidazol-5-yl}carbamic acid

Traditional Name

3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]imidazol-4-ylcarbamic acid

CAS Registry Number

Not Available

SMILES

[H][C@]1(COP(O)(O)=O)O[C@@]([H])(N2C=NC=C2NC(O)=O)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C9H14N3O9P/c13-6-4(2-20-22(17,18)19)21-8(7(6)14)12-3-10-1-5(12)11-9(15)16/h1,3-4,6-8,11,13-14H,2H2,(H,15,16)(H2,17,18,19)/t4-,6-,7-,8-/m1/s1

InChI Key

JHLXDWGVSYMXPL-XVFCMESISA-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
Imidazole ribonucleoside
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Monoalkyl phosphate
N-substituted imidazole
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Azole
Tetrahydrofuran
Imidazole
Heteroaromatic compound
1,2-diol
Secondary alcohol
Carbamic acid
Carbamic acid derivative
Carbonic acid derivative
Oxacycle
Azacycle
Organoheterocyclic compound
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Carbonyl group
Hydrocarbon derivative
Alcohol
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

1-(phosphoribosyl)imidazole (CHEBI:48000 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	2.61 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-3.4	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	1.18	ChemAxon
pKa (Strongest Basic)	5.83	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	183.6 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	67.45 m³·mol⁻¹	ChemAxon
Polarizability	28.23 Å³	ChemAxon
Number of Rings	2	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

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
Bacteria/Eubacteria	Proteobacteria	10	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig	Unknown
Bacteria/Eubacteria	Aquificae	1
Bacteria/Eubacteria	Firmicutes	11	Human feces; Human
Bacteria/Eubacteria	Actinobacteria	5	Human ; Cattle
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig	Unknown
Archaea/Archaea	Euryarchaeota	4	Human feces; Human
Archaea	Euryarchaeota	1	Human feces; Human
Archaea	Crenarchaeota	1
Bacteria	nah	1
Bacteria/Eubacteria	Thermotogae	1
Bacteria/Eubacteria	Cyanobacteria	1

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

C15667

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

23657851

PDB ID

Not Available

ChEBI ID

48000

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 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole (MMDBc0031731)

MOL for #<Metabolite:0x00007f9221f5a680>

3D MOL for #<Metabolite:0x00007f9221f5a680>

3D SDF for #<Metabolite:0x00007f9221f5a680>

3D-SDF for #<Metabolite:0x00007f9221f5a680>

PDB for #<Metabolite:0x00007f9221f5a680>

3D PDB for #<Metabolite:0x00007f9221f5a680>

SMILES for #<Metabolite:0x00007f9221f5a680>

INCHI for #<Metabolite:0x00007f9221f5a680>

Structure for #<Metabolite:0x00007f9221f5a680>

3D Structure for #<Metabolite:0x00007f9221f5a680>