ECMDB: 5-Aminoimidazole ribonucleotide (ECMDB01235) (M2MDB000306)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (3)XML

Proteins (1025)

Record Information

Version

2.0

Creation Date

2012-05-31 13:48:06 -0600

Update Date

2015-06-03 15:53:52 -0600

Secondary Accession Numbers

ECMDB01235

Identification

Name:

5-Aminoimidazole ribonucleotide

Description

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

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms:

1-(5'-Phosphoribosyl)-5-aminoimidazole
1-(5-Phospho-D-ribosyl)-5-aminoimidazole
5'-Phosphoribosyl-5-aminoimidazole
5-Amino-1-(5-phospho-D-ribosyl)imidazole
5-Amino-1-(5-phospho-β-D-ribosyl)imidazole
5-Aminoimidazole ribonucleotide
5-Aminoimidazole ribotide
AIR
Aminoimidazole ribotide
Phosphoribosylaminoimidazole

Chemical Formula:

C₈H₁₄N₃O₇P

Weight:

Average: 295.1864
Monoisotopic: 295.056936329

InChI Key:

PDACUKOKVHBVHJ-XVFCMESISA-N

InChI:

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

CAS number:

25635-88-5

IUPAC Name:

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

Traditional IUPAC Name:

5-aminoimidazole ribotide

SMILES:

NC1=CN=CN1[C@@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

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

Not Available

Physical Properties

State:

Solid

Charge:

-1

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

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	24.79 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

SMPDB Pathways:

Thiamin diphosphate biosynthesis	PW002028
purine nucleotides de novo biosynthesis	PW000910
purine nucleotides de novo biosynthesis 1435709748	PW000960
purine nucleotides de novo biosynthesis 2	PW002033

KEGG Pathways:

Metabolic pathways eco01100
Purine metabolism ec00230
Thiamine metabolism ec00730

EcoCyc Pathways:

4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis PWY-6890
5-aminoimidazole ribonucleotide biosynthesis I PWY-6121
5-aminoimidazole ribonucleotide biosynthesis II PWY-6122
inosine-5'-phosphate biosynthesis I PWY-6123
superpathway of 5-aminoimidazole ribonucleotide biosynthesis PWY-6277

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9310000000-83cf50bc3f675ec17ccb	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-01vk-9314000000-ed8269ba053b2e3a4fc4	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-9130000000-143cf7dfaf8cc77d6280	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9000000000-26b4d68163a88586005b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9000000000-87449f0e16a1690c4873	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0036-9160000000-50e60dc03e3bb2050636	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0059-9000000000-797c3e0faf96fe4330aa	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-9e3a71c432cedbcd3892	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-2490000000-7dd58fcac26f75e7c46f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-9000000000-6dd5f8e7028cd1ab65d2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9000000000-7542d4d80a10b03631f0	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002f-9080000000-e3666a5af349af6427f9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-2dd173dfe9a30642b89d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-7c5243a801196e080ddb	View in MoNA
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

Chang HK, Weber ME, King M: Mucus transport by high-frequency nonsymmetrical oscillatory airflow. J Appl Physiol. 1988 Sep;65(3):1203-9. Pubmed: 3182490
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Lawhorn, B. G., Mehl, R. A., Begley, T. P. (2004). "Biosynthesis of the thiamin pyrimidine: the reconstitution of a remarkable rearrangement reaction." Org Biomol Chem 2:2538-2546. Pubmed: 15326535
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. Pubmed: 10511267
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
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. Pubmed: 9744758

Synthesis Reference:

Groziak M P; Bhat B; Leonard N J Nonenzymatic synthesis of 5-aminoimidazole ribonucleoside and recognition of its facile rearrangement. Proceedings of the National Academy of Sciences of the United States of America (1988), 85(19), 7174-6.

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	28843
HMDB ID	HMDB01235
Pubchem Compound ID	161500
Kegg ID	C03373
ChemSpider ID	141854
Wikipedia ID	5-Aminoimidazole_ribotide
BioCyc ID	5-PHOSPHORIBOSYL-5-AMINOIMIDAZOLE
EcoCyc ID	5-PHOSPHORIBOSYL-5-AMINOIMIDAZOLE
Ligand Expo	AIR

Enzymes

Protein Details

1. Phosphoribosylformylglycinamidine cyclo-ligase

General function:: Involved in catalytic activity
Specific function:: ATP + 2-(formamido)-N(1)-(5-phospho-D- ribosyl)acetamidine = ADP + phosphate + 5-amino-1-(5-phospho-D- ribosyl)imidazole
Gene Name:: purM
Uniprot ID:: P08178
Molecular weight:: 36854

Reactions

ATP + 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine = ADP + phosphate + 5-amino-1-(5-phospho-D-ribosyl)imidazole.

Protein Details

2. Phosphoribosylaminoimidazole carboxylase ATPase subunit

General function:: Involved in phosphoribosylaminoimidazole carboxylase activity
Specific function:: Possesses an ATPase activity that is dependent on the presence of AIR (aminoimidazole ribonucleotide). The association of purK and purE produces an enzyme complex capable of converting AIR to CAIR efficiently under physiological condition
Gene Name:: purK
Uniprot ID:: P09029
Molecular weight:: 39461

Reactions

ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO(3)(-) = ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole.

Protein Details

3. Phosphomethylpyrimidine synthase

General function:: Involved in thiamine biosynthetic process
Specific function:: Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction
Gene Name:: thiC
Uniprot ID:: P30136
Molecular weight:: 70850

Reactions

5-amino-1-(5-phospho-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-phosphomethylpyrimidine + 5'-deoxyadenosine + L-methionine + formate + CO.

5-Aminoimidazole ribonucleotide (ECMDB01235) (M2MDB000306)

Structure for #<Compound:0xac3b6e04>

Enzymes

Reactions

Reactions

Reactions