MiMeDB: Showing metabocard for 5-Phosphoribosyl-5-carboxyaminoimidazole (MMDBc0031587)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:40:26 UTC

Update Date

2022-08-31 18:21:59 UTC

Metabolite ID

MMDBc0031587

Metabolite Identification

Common Name

5-Phosphoribosyl-5-carboxyaminoimidazole

Description

5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole is an intermediate in purine metabolism and IMP biosynthesis via the de novo pathway. It is a substrate of the PurK enzyme which catalyzes the ATP-dependent conversion of 5-aminoimidazole ribonucleotide (AIR) and HCO3- to N5-carboxyaminoimidazole ribonucleotide (N5-CAIR).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 08141218142D          

 22 23  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  0  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  0  0  0  0  0  0  0  0  0  0
   -0.8631    2.5189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1956    3.0038    0.0000 C   0  0  0  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  5  0  0  0  0  0  0  0  0  0  0
   -2.3948    6.5444    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.2424    6.3619    0.0000 O   0  5  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
  4  2  1  0  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
 12  8  1  0  0  0  0
 13  6  1  0  0  0  0
 14  7  1  0  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
M  CHG  3  16  -1  17  -1  18  -1
M  END
> <DATABASE_ID>
MMDBc0031587

> <DATABASE_NAME>
MIME

> <SMILES>
OC1C(O)C(OC1COP([O-])([O-])=O)N1C=NC=C1NC([O-])=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)/p-3

> <INCHI_KEY>
JHLXDWGVSYMXPL-UHFFFAOYSA-K

> <FORMULA>
C9H11N3O9P

> <MOLECULAR_WEIGHT>
336.1721

> <EXACT_MASS>
336.023290477

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
27.047823226787152

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-(1-{3,4-dihydroxy-5-[(phosphonatooxy)methyl]oxolan-2-yl}-1H-imidazol-5-yl)carbamate

> <ALOGPS_LOGP>
-1.15

> <JCHEM_LOGP>
-3.4212731610733864

> <ALOGPS_LOGS>
-1.85

> <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>
192.08999999999997

> <JCHEM_REFRACTIVITY>
76.04649999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.52e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-(3-{3,4-dihydroxy-5-[(phosphonatooxy)methyl]oxolan-2-yl}imidazol-4-yl)carbamate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 14-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-AUG-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-1
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O-1
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
CONECT    1    5   10                                                       
CONECT    2    4   20                                                       
CONECT    3   10   12                                                       
CONECT    4    2    6   21                                                  
CONECT    5    1   11   12                                                  
CONECT    6    4    7   13                                                  
CONECT    7    6    8   14                                                  
CONECT    8    7   12   21                                                  
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                                             
MASTER        0    0    0    0    0    0    0    0   22    0   46    0
END

Synonyms

Not Available

Molecular Formula

C₉H₁₁N₃O₉P

Average Mass

336.1721

Monoisotopic Mass

336.023290477

IUPAC Name

N-(1-{3,4-dihydroxy-5-[(phosphonatooxy)methyl]oxolan-2-yl}-1H-imidazol-5-yl)carbamate

Traditional Name

N-(3-{3,4-dihydroxy-5-[(phosphonatooxy)methyl]oxolan-2-yl}imidazol-4-yl)carbamate

CAS Registry Number

Not Available

SMILES

OC1C(O)C(OC1COP([O-])([O-])=O)N1C=NC=C1NC([O-])=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)/p-3

InChI Key

JHLXDWGVSYMXPL-UHFFFAOYSA-K

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

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

a small molecule (CPD0-181 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	5.52 g/L	ALOGPS
logP	-1.2	ALOGPS
logP	-3.4	ChemAxon
logS	-1.8	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	3	ChemAxon
Polar Surface Area	192.09 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	76.05 m³·mol⁻¹	ChemAxon
Polarizability	27.05 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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	splash10-000i-0009000000-59a258785315de737eb7	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001r-0119000000-3c24b671f00e253952c9	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000y-7920000000-71a059951733c823f7e9	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0009000000-357eaf776f2045653354	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-000i-3119000000-a5ab9eda349cf23bb092	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-003s-9000000000-648a69b10d5145733551	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	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
MMDBr0019209	5-Phosphoribosyl-5-carboxyaminoimidazole	5-Amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate	N5-carboxyaminoimidazole ribonucleotide mutase		PathBank	31602464
MMDBr0019210	Hydrogen carbonate	Hydrogen Ion	N5-carboxyaminoimidazole ribonucleotide synthase	Synthesis	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	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	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

25244287

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 5-Phosphoribosyl-5-carboxyaminoimidazole (MMDBc0031587)

MOL for #<Metabolite:0x00007fa4e3729068>

3D MOL for #<Metabolite:0x00007fa4e3729068>

3D SDF for #<Metabolite:0x00007fa4e3729068>

3D-SDF for #<Metabolite:0x00007fa4e3729068>

PDB for #<Metabolite:0x00007fa4e3729068>

3D PDB for #<Metabolite:0x00007fa4e3729068>

SMILES for #<Metabolite:0x00007fa4e3729068>

INCHI for #<Metabolite:0x00007fa4e3729068>

Structure for #<Metabolite:0x00007fa4e3729068>

3D Structure for #<Metabolite:0x00007fa4e3729068>