MiMeDB: Showing metabocard for 5-Amino-1-(5-phospho-D-ribosyl)imidazole (MMDBc0033005)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:30:48 UTC

Update Date

2024-04-20 06:09:07 UTC

Metabolite ID

MMDBc0033005

Metabolite Identification

Common Name

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

Description

5-aminoimidazole ribonucleotide (AIR), is an intermediate of purine nucleotide biosynthesis. It is also the precursor to 4-amino-2-methyl-5-hydroxymethylpyrimidine (HMP), the first product of pyrimidine biosynthesis. This reaction is mediated by the enzyme HMP-P kinase (ThiD). HMP is a precursor of thiamine phosphate (TMP), and subsequently to thiamine pyrophosphate (TPP). TPP is an essential cofactor in all living systems that plays a central role in metabolism. (PMID: 15326535 ). 5-Aminoimidazole ribonucleotide is a substrate for a number of proteins including: Scaffold attachment factor B2, Multifunctional protein ADE2, Pulmonary surfactant-associated protein B, Tumor necrosis factor receptor superfamily member 25, Pulmonary surfactant-associated protein C, Serine/threonine-protein kinase Chk1, Vinexin, Trifunctional purine biosynthetic protein adenosine-3, Antileukoproteinase 1 and Scaffold attachment factor B.

Structure

MOL SDF PDB SMILES InChI

ChEBI
  Mrv0541 02241222212D          

 19 20  0  0  1  0            999 V2000
   17.6022  -18.1117    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.0147  -19.3812    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.4272  -20.0957    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1897  -19.3812    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.7772  -20.0957    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.9348  -18.5967    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   16.2203  -18.1842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5058  -18.5967    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.6808  -17.7717    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.8558  -18.5967    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.6808  -18.5967    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   14.6808  -19.4217    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2696  -18.5967    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.7007  -17.0580    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.7829  -18.3903    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9841  -18.1842    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.2258  -17.6943    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.9333  -17.3608    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2188  -16.9483    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  1 13  1  0  0  0  0
  6  4  1  0  0  0  0
  4  2  1  0  0  0  0
  2 13  1  0  0  0  0
  2  3  1  6  0  0  0
  4  5  1  6  0  0  0
  6  7  1  1  0  0  0
  7  8  1  0  0  0  0
  8 11  1  0  0  0  0
 11  9  2  0  0  0  0
 11 10  1  0  0  0  0
 11 12  1  0  0  0  0
 13 16  1  0  0  0  0
 14 18  2  0  0  0  0
 14 17  1  0  0  0  0
 18 16  1  0  0  0  0
 16 15  1  0  0  0  0
 15 17  2  0  0  0  0
 18 19  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033005

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=CN=CN1C1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C8H14N3O7P/c9-5-1-10-3-11(5)8-7(13)6(12)4(18-8)2-17-19(14,15)16/h1,3-4,6-8,12-13H,2,9H2,(H2,14,15,16)/t4-,6-,7-,8?/m1/s1

> <INCHI_KEY>
PDACUKOKVHBVHJ-ZRTZXPPTSA-N

> <FORMULA>
C8H14N3O7P

> <MOLECULAR_WEIGHT>
295.1864

> <EXACT_MASS>
295.056936329

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
25.10134334229274

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-2.27

> <JCHEM_LOGP>
-4.327418831783963

> <ALOGPS_LOGS>
-1.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.241083773689428

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2247156062018343

> <JCHEM_PKA_STRONGEST_BASIC>
7.918025333249561

> <JCHEM_POLAR_SURFACE_AREA>
160.29000000000005

> <JCHEM_REFRACTIVITY>
60.435700000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.38e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
aminoimidazole ribotide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: ChEBI                                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0      32.857 -33.809   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      33.627 -36.178   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      34.397 -37.512   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      32.087 -36.178   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      31.317 -37.512   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      31.612 -34.714   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      30.278 -33.944   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      28.944 -34.714   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      27.404 -33.174   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      25.864 -34.714   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0      27.404 -34.714   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0      27.404 -36.254   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      34.103 -34.714   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      36.775 -31.842   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      36.928 -34.329   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      35.437 -33.944   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0      37.755 -33.029   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      35.342 -32.407   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      34.008 -31.637   0.000  0.00  0.00           N+0
CONECT    1    6   13                                                       
CONECT    2    4   13    3                                                  
CONECT    3    2                                                            
CONECT    4    6    2    5                                                  
CONECT    5    4                                                            
CONECT    6    1    4    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7   11                                                       
CONECT    9   11                                                            
CONECT   10   11                                                            
CONECT   11    8    9   10   12                                             
CONECT   12   11                                                            
CONECT   13    1    2   16                                                  
CONECT   14   18   17                                                       
CONECT   15   16   17                                                       
CONECT   16   13   18   15                                                  
CONECT   17   14   15                                                       
CONECT   18   14   16   19                                                  
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

Synonyms

Value	Source
1-(5'-Phosphoribosyl)-5-aminoimidazole	ChEBI
1-(5-phospho-D-Ribosyl)-5-aminoimidazole	ChEBI
5'-Phosphoribosyl-5-aminoimidazole	ChEBI
AIR	ChEBI

Molecular Formula

C₈H₁₄N₃O₇P

Average Mass

295.1864

Monoisotopic Mass

295.056936329

IUPAC Name

{[(2R,3S,4R)-5-(5-amino-1H-imidazol-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional Name

aminoimidazole ribotide

CAS Registry Number

25635-88-5

SMILES

NC1=CN=CN1C1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C8H14N3O7P/c9-5-1-10-3-11(5)8-7(13)6(12)4(18-8)2-17-19(14,15)16/h1,3-4,6-8,12-13H,2,9H2,(H2,14,15,16)/t4-,6-,7-,8?/m1/s1

InChI Key

PDACUKOKVHBVHJ-ZRTZXPPTSA-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
Aminoimidazole
Alkyl phosphate
Phosphoric acid ester
N-substituted imidazole
Organic phosphoric acid derivative
Heteroaromatic compound
Azole
Tetrahydrofuran
Imidazole
1,2-diol
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Azacycle
Organic oxide
Primary amine
Organic nitrogen compound
Alcohol
Hydrocarbon derivative
Amine
Organopnictogen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

1-(phosphoribosyl)imidazole (CHEBI:28843 )
aminoimidazole (CHEBI:28843 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	3.38 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-4.3	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	1.22	ChemAxon
pKa (Strongest Basic)	7.92	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	160.29 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	60.44 m³·mol⁻¹	ChemAxon
Polarizability	25.1 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 GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9310000000-83cf50bc3f675ec17ccb	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-9130000000-125365b6a6266dc5c7d8	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9000000000-017dd2a339fc8f5491f8	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9000000000-8cfa527f76f0a0e8bc26	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0036-9160000000-92a2872e7cf8912c8f0f	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0059-9000000000-818588cb1fbe6ad37863	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-57676c13a6614d36fe6d	2016-09-12	View Spectrum

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

Not Available

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
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	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

16048619

PDB ID

Not Available

ChEBI ID

28843

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Chang HK, Weber ME, King M: Mucus transport by high-frequency nonsymmetrical oscillatory airflow. J Appl Physiol (1985). 1988 Sep;65(3):1203-9. doi: 10.1152/jappl.1988.65.3.1203. [PubMed:3182490 ]
Vetvik H, Grewal HM, Haugen IL, Ahren C, Haneberg B: Mucosal antibodies can be measured in air-dried samples of saliva and feces. J Immunol Methods. 1998 Jun 1;215(1-2):163-72. doi: 10.1016/s0022-1759(98)00089-1. [PubMed:9744758 ]
Ogata M, Michitsuji H, Fujiki Y: Estimating amounts of toluene inhaled by workers with protective mask using biological indicators of toluene. Toxicol Lett. 1999 Sep 5;108(2-3):233-9. doi: 10.1016/s0378-4274(99)00094-6. [PubMed:10511267 ]
Lawhorn BG, Mehl RA, Begley TP: Biosynthesis of the thiamin pyrimidine: the reconstitution of a remarkable rearrangement reaction. Org Biomol Chem. 2004 Sep 7;2(17):2538-46. doi: 10.1039/B405429F. Epub 2004 Aug 11. [PubMed:15326535 ]

Showing metabocard for 5-Amino-1-(5-phospho-D-ribosyl)imidazole (MMDBc0033005)

MOL for #<Metabolite:0x00007fed1535fe80>

3D MOL for #<Metabolite:0x00007fed1535fe80>

3D SDF for #<Metabolite:0x00007fed1535fe80>

3D-SDF for #<Metabolite:0x00007fed1535fe80>

PDB for #<Metabolite:0x00007fed1535fe80>

3D PDB for #<Metabolite:0x00007fed1535fe80>

SMILES for #<Metabolite:0x00007fed1535fe80>

INCHI for #<Metabolite:0x00007fed1535fe80>

Structure for #<Metabolite:0x00007fed1535fe80>

3D Structure for #<Metabolite:0x00007fed1535fe80>