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(2S)-2-[5-Amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinic acid (YMDB00561)

Identification
YMDB IDYMDB00561
Name(2S)-2-[5-Amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinic acid
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description(2S)-2-[5-Amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinic acid belongs to the class of organic compounds known as 1-ribosyl-imidazolecarboxamides. These are organic compounds containing the imidazole ring linked to a ribose ring through a 1-2 bond (2S)-2-[5-Amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinic acid is a strong basic compound (based on its pKa) (2S)-2-[5-Amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinic acid may be a unique S. cerevisiae (yeast) metabolite.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinic acid
  • (S)-2-[5-Amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido]succinate
  • 1-(5'-Phosphoribosyl)-4-(N-succinocarboxamide)-5-aminoimidazole
  • 1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole
  • 5-Amino-4-imidazole-N-succinocarboxamide ribonucleotide
  • 5-phosphoribosyl-4-(n-succinocarboxamide)-5-aminoimidazole
  • 5'-Phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole
  • 5'-Phosphoribosyl-4-(N-succinocarbozamide)-5-aminoimidazole
  • Phosphoribosylaminoimidazolesuccinocarboxamide
  • SAICAR
  • SAICAriboside
  • Succino-AICAR
  • Succinylaminoimidazole carboxamide riboside
  • (2S)-2-[5-Amino-1-(5-phospho-b-D-ribosyl)imidazole-4-carboxamido]succinate
  • (2S)-2-[5-Amino-1-(5-phospho-b-D-ribosyl)imidazole-4-carboxamido]succinic acid
  • (2S)-2-[5-Amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate
  • (2S)-2-[5-Amino-1-(5-phospho-β-D-ribosyl)imidazole-4-carboxamido]succinate
  • (2S)-2-[5-Amino-1-(5-phospho-β-D-ribosyl)imidazole-4-carboxamido]succinic acid
CAS number3031-95-6
WeightAverage: 454.2833
Monoisotopic: 454.073708604
InChI KeyNAQGHJTUZRHGAC-LBGUGVGYSA-N
InChIInChI=1S/C13H19N4O12P/c14-10-7(11(22)16-4(13(23)24)1-6(18)19)15-3-17(10)12-9(21)8(20)5(29-12)2-28-30(25,26)27/h3-5,8-9,12,20-21H,1-2,14H2,(H,16,22)(H,18,19)(H,23,24)(H2,25,26,27)/t4?,5-,8-,9-,12-/m1/s1
IUPAC Name2-({5-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-1H-imidazol-4-yl}formamido)butanedioic acid
Traditional IUPAC Name2-({5-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]imidazol-4-yl}formamido)butanedioic acid
Chemical FormulaC13H19N4O12P
SMILESNC1=C(N=CN1[C@@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O)C(=O)NC(CC(O)=O)C(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as 1-ribosyl-imidazolecarboxamides. These are organic compounds containing the imidazole ring linked to a ribose ring through a 1-2 bond.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassImidazole ribonucleosides and ribonucleotides
Sub Class1-ribosyl-imidazolecarboxamides
Direct Parent1-ribosyl-imidazolecarboxamides
Alternative Parents
Substituents
  • 1-ribosyl-imidazolecarboxamide
  • Pentose-5-phosphate
  • Pentose phosphate
  • Aspartic acid or derivatives
  • N-acyl-alpha amino acid or derivatives
  • N-acyl-alpha-amino acid
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Alpha-amino acid or derivatives
  • Pentose monosaccharide
  • 2-heteroaryl carboxamide
  • Imidazolyl carboxylic acid derivative
  • Imidazole-4-carbonyl group
  • Monoalkyl phosphate
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Alkyl phosphate
  • Dicarboxylic acid or derivatives
  • Phosphoric acid ester
  • Aminoimidazole
  • Monosaccharide
  • Imidazole
  • Heteroaromatic compound
  • Azole
  • Vinylogous amide
  • Tetrahydrofuran
  • Amino acid or derivatives
  • Carboxamide group
  • Amino acid
  • 1,2-diol
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Carboxylic acid
  • Alcohol
  • Organic oxygen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Amine
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility1.73 g/LALOGPS
logP-1.8ALOGPS
logP-4.8ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)1.22ChemAxon
pKa (Strongest Basic)4.54ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area263.99 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity90.65 m³·mol⁻¹ChemAxon
Polarizability37.61 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
purine nucleotides de novo biosynthesisPW002478 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Purine metabolismec00230 Map00230
SMPDB ReactionsNot Available
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-055o-1592600000-05db249dfb0f14143f9fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-3950000000-6ebf6a64483dd1392782JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001l-5940000000-e218e278f5195eb90341JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0ug3-6381900000-4fec69ff813fe652ea7dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004j-9350000000-e4e387627fbca1ef1201JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-95f6153e96335a5d2b32JSpectraViewer
MSMass Spectrum (Electron Ionization)Not AvailableJSpectraViewer
References
References:
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID18319
HMDB IDHMDB00797
Pubchem Compound ID160666
Kegg IDC04823
ChemSpider ID389419
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDP-RIBOSYL-4-SUCCCARB-AMINOIMIDAZOLE

Enzymes

Protein Details
1. Adenylosuccinate lyase
General function:
Involved in catalytic activity
Specific function:
N(6)-(1,2-dicarboxyethyl)AMP = fumarate + AMP
Gene Name:
ADE13
Uniprot ID:
Q05911
Molecular weight:
54509.89844
Reactions
N(6)-(1,2-dicarboxyethyl)AMP → fumarate + AMP.
(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate → fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide.
Protein Details
2. Phosphoribosylaminoimidazole-succinocarboxamide synthase
General function:
Involved in ATP binding
Specific function:
ATP + 5-amino-1-(5-phospho-D- ribosyl)imidazole-4-carboxylate + L-aspartate = ADP + phosphate + (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido)succinate
Gene Name:
ADE1
Uniprot ID:
P27616
Molecular weight:
34603.10156
Reactions
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate → ADP + phosphate + (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate.