(S)-Methylmalonyl-CoA (ECMDB02310) (M2MDB000456)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (381)
Record Information
Version2.0
Creation Date2012-05-31 13:56:34 -0600
Update Date2015-10-15 16:13:59 -0600
Secondary Accession Numbers
  • ECMDB02310
Identification
Name:(S)-Methylmalonyl-CoA
DescriptionMethylmalonyl-CoA is an intermediate in the metabolism of Propanoate.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • (2S)-methyl-malonyl-CoA
  • (R)-methylmalonyl-CoA
  • (R)-methylmalonyl-Coenzyme A
  • (S)-2-Methyl-3-Oxopropanoyl-Coa
  • (S)-methyl-malonyl-CoA
  • (S)-methyl-malonyl-Coenzyme A
  • CH3-malonyl-CoA
  • CH3-malonyl-Coenzyme A
  • D-Methylmalonyl-CoA
  • D-Methylmalonyl-Coenzyme A
  • L-Methylmalonyl-CoA
  • L-Methylmalonyl-Coenzyme A
  • Methyl-malonyl-coenzyme A
Chemical Formula:C25H40N7O19P3S
Weight:Average: 867.607
Monoisotopic: 867.131252359
InChI Key:MZFOKIKEPGUZEN-JDVCRUKVSA-N
InChI:InChI=1S/C25H40N7O19P3S/c1-12(23(37)38)24(39)55-7-6-27-14(33)4-5-28-21(36)18(35)25(2,3)9-48-54(45,46)51-53(43,44)47-8-13-17(50-52(40,41)42)16(34)22(49-13)32-11-31-15-19(26)29-10-30-20(15)32/h10-13,16-18,22,34-35H,4-9H2,1-3H3,(H,27,33)(H,28,36)(H,37,38)(H,43,44)(H,45,46)(H2,26,29,30)(H2,40,41,42)/t12-,13?,16+,17+,18-,22?/m0/s1
CAS number:104809-02-1
IUPAC Name:(2S)-3-({2-[(3-{[(2R)-4-({[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-1,2-dihydroxy-3,3-dimethylbutylidene]amino}-1-hydroxypropylidene)amino]ethyl}sulfanyl)-2-methyl-3-oxopropanoic acid
Traditional IUPAC Name:(2S)-3-({2-[(3-{[(2R)-4-[({[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,2-dihydroxy-3,3-dimethylbutylidene]amino}-1-hydroxypropylidene)amino]ethyl}sulfanyl)-2-methyl-3-oxopropanoic acid
SMILES:C[C@@H](C(O)=O)C(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC1OC([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C(N)N=CN=C12
Chemical Taxonomy
Description belongs to the class of organic compounds known as acyl coas. These are organic compounds containing a coenzyme A substructure linked to an acyl chain.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acyl thioesters
Direct ParentAcyl CoAs
Alternative Parents
Substituents
  • Coenzyme a or derivatives
  • Purine ribonucleoside 3',5'-bisphosphate
  • Purine ribonucleoside bisphosphate
  • Purine ribonucleoside diphosphate
  • Ribonucleoside 3'-phosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Beta amino acid or derivatives
  • Glycosyl compound
  • N-glycosyl compound
  • 6-aminopurine
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Pentose monosaccharide
  • Imidazopyrimidine
  • Purine
  • Monoalkyl phosphate
  • Aminopyrimidine
  • Alkyl phosphate
  • 1,3-dicarbonyl compound
  • Imidolactam
  • N-acyl-amine
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Monosaccharide
  • Pyrimidine
  • Fatty amide
  • Phosphoric acid ester
  • Tetrahydrofuran
  • Imidazole
  • Heteroaromatic compound
  • Azole
  • Thiocarboxylic acid ester
  • Carbothioic s-ester
  • Secondary alcohol
  • Amino acid
  • Carboxamide group
  • Amino acid or derivatives
  • Secondary carboxylic acid amide
  • Organoheterocyclic compound
  • Sulfenyl compound
  • Thiocarboxylic acid or derivatives
  • Azacycle
  • Oxacycle
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic oxygen compound
  • Primary amine
  • Hydrocarbon derivative
  • Carbonyl group
  • Organosulfur compound
  • Organopnictogen compound
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Alcohol
  • Amine
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-4
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility5.49 g/LALOGPS
logP-0.4ALOGPS
logP-3.9ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)0.82ChemAxon
pKa (Strongest Basic)4.82ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count21ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area407.91 ŲChemAxon
Rotatable Bond Count22ChemAxon
Refractivity184.17 m³·mol⁻¹ChemAxon
Polarizability75.96 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Succinyl-CoA > (S)-Methylmalonyl-CoA
Hydrogen ion + (S)-Methylmalonyl-CoA <> Carbon dioxide + Propionyl-CoA
(S)-Methylmalonyl-CoA <> Propionyl-CoA + Carbon dioxide
R-Methylmalonyl-CoA <> (S)-Methylmalonyl-CoA
Adenosine triphosphate + Hydrogen carbonate + Propionyl-CoA > Hydrogen ion + ADP + Phosphate + (S)-Methylmalonyl-CoA
(S)-Methylmalonyl-CoA > Propionyl-CoA + Carbon dioxide
SMPDB Pathways:
Propanoate metabolismPW000940 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
  • Glyoxylate and dicarboxylate metabolism ec00630
  • Microbial metabolism in diverse environments ec01120
  • Propanoate metabolism ec00640
  • Valine, leucine and isoleucine degradation ec00280
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-3931000120-503dfdefbc3bdbb5e1bcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-002r-1911000000-cd0632f31aad1955e31eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-3910000000-6b360fd99bac9c77be27View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00l2-9811041650-6ff1106e71f7373df82dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-003r-4911110010-0041cbe45f5267a47176View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-057i-6900100000-da5c7610b3b97c5fb82fView in MoNA
References
References:
  • 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
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID15466
HMDB IDHMDB01269
Pubchem Compound ID613
Kegg IDC00683
ChemSpider ID388424
WikipediaMethylmalonyl-CoA
BioCyc IDD-METHYL-MALONYL-COA
EcoCyc IDD-METHYL-MALONYL-COA

Enzymes

Protein Details
1. Protein sbm
General function:
Involved in isomerase activity
Specific function:
Specific function unknown
Gene Name:
sbm
Uniprot ID:
P27253
Molecular weight:
77871
Reactions
(R)-methylmalonyl-CoA = succinyl-CoA.
Protein Details
2. Methylmalonyl-CoA decarboxylase
General function:
Involved in catalytic activity
Specific function:
(S)-methylmalonyl-CoA = propanoyl-CoA + CO(2)
Gene Name:
mmcD
Uniprot ID:
P52045
Molecular weight:
29172
Reactions
(S)-methylmalonyl-CoA = propanoyl-CoA + CO(2).