Showing metabocard for S-Methylmalonyl-CoA (BMDB0002310)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (3) Show 3 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:53:57 UTC
Update Date2020-05-21 16:28:45 UTC
BMDB IDBMDB0002310
Secondary Accession Numbers
  • BMDB02310
Metabolite Identification
Common NameS-Methylmalonyl-CoA
DescriptionS-Methylmalonyl-CoA 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. Based on a literature review very few articles have been published on S-Methylmalonyl-CoA.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(S)-Methylmalonyl-CoAHMDB
(S)-Methylmalonyl-coenzyme AHMDB
Chemical FormulaC25H40N7O19P3S
Average Molecular Weight867.607
Monoisotopic Molecular Weight867.131252359
IUPAC Name(2S)-3-[(2-{3-[(2R)-3-[({[({[(3S,4R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)methyl]-2-hydroxy-3-methylbutanamido]propanamido}ethyl)sulfanyl]-2-methyl-3-oxopropanoic acid
Traditional Name(2S)-3-[(2-{3-[(2R)-3-{[({[(3S,4R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]methyl}-2-hydroxy-3-methylbutanamido]propanamido}ethyl)sulfanyl]-2-methyl-3-oxopropanoic acid
CAS Registry Number73173-91-8
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
InChI Identifier
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
InChI KeyMZFOKIKEPGUZEN-JDVCRUKVSA-N
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 DescriptorsNot Available
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
  • Exogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cell membrane
  • Cytoplasm
  • Membrane
  • Mitochondria
  • Peroxisome
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.6ALOGPS
logP-6.5ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)0.82ChemAxon
pKa (Strongest Basic)4.97ChemAxon
Physiological Charge-5ChemAxon
Hydrogen Acceptor Count19ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area400.93 ŲChemAxon
Rotatable Bond Count22ChemAxon
Refractivity183.13 m³·mol⁻¹ChemAxon
Polarizability76.39 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-4911000020-c392edc35bfe7a605c16View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-1913000000-d7d73fa71a22c4b9e10cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-2911000000-1c3ee05de5b5cf1c067cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00nb-9811140550-fade85d2dd723fe43fdaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-5911110010-2c7ce12039a0e299c300View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a7i-5900100000-48f1904d8b30fe71d5e4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-0000000190-f076790ab423a5aa6698View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0gc0-1301103960-0fda0df24a3a3ad7fe59View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-1159000000-2510a377524f6c35c5f2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0000000490-c603c70c007f70ef33b6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000i-9100001110-8a105fab331fa01db259View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0f9b-6003404900-356070eb7375b08b8e14View in MoNA
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cell membrane
  • Cytoplasm
  • Membrane
  • Mitochondria
  • Peroxisome
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0002310
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022959
KNApSAcK IDNot Available
Chemspider ID13628334
KEGG Compound IDC00683
BioCyc IDNot Available
BiGG ID35689
Wikipedia LinkMethylmalonyl-CoA
METLIN ID6609
PubChem Compound21252287
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceMutka, Sarah C.; Bondi, Shana M.; Carney, John R.; Da Silva, Nancy A.; Kealey, James T. Metabolic pathway engineering for complex polyketide biosynthesis in Saccharomyces cerevisiae .FEMS Yeast Research (2006), 6(1), 40-47.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Propionyl-CoA carboxylase beta chain, mitochondrial
General function:
Involved in ATP binding
Specific function:
This is one of the 2 subunits of the biotin-dependent propionyl-CoA carboxylase (PCC), a mitochondrial enzyme involved in the catabolism of odd chain fatty acids, branched-chain amino acids isoleucine, threonine, methionine, and valine and other metabolites. Propionyl-CoA carboxylase catalyzes the carboxylation of propionyl-CoA/propanoyl-CoA to D-methylmalonyl-CoA/(S)-methylmalonyl-CoA (By similarity). Within the holoenzyme, the alpha subunit catalyzes the ATP-dependent carboxylation of the biotin carried by the biotin carboxyl carrier (BCC) domain, while the beta subunit then transfers the carboxyl group from carboxylated biotin to propionyl-CoA (By similarity). Propionyl-CoA carboxylase also significantly acts on butyryl-CoA/butanoyl-CoA, which is converted to ethylmalonyl-CoA/(2S)-ethylmalonyl-CoA (By similarity). Other alternative minor substrates include (2E)-butenoyl-CoA/crotonoyl-CoA (By similarity).
Gene Name:
PCCB
Uniprot ID:
Q2TBR0
Molecular weight:
58311.0
Reactions
Propionyl-CoA + Adenosine triphosphate + Hydrogen carbonate → S-Methylmalonyl-CoA + ADP + Hydrogen phosphatedetails
Propionyl-CoA + Hydrogen carbonate + Adenosine triphosphate → S-Methylmalonyl-CoA + ADP + Hydrogendetails
Enzyme Details
2. Methylmalonyl-CoA epimerase, mitochondrial
General function:
Amino acid transport and metabolism
Specific function:
Not Available
Gene Name:
MCEE
Uniprot ID:
Q2KIZ3
Molecular weight:
18514.0
Reactions
S-Methylmalonyl-CoA → R-Methylmalonyl-CoAdetails
Enzyme Details
3. Pyruvate carboxylase, mitochondrial
General function:
Involved in ATP binding
Specific function:
Pyruvate carboxylase catalyzes a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second. Catalyzes in a tissue specific manner, the initial reactions of glucose (liver, kidney) and lipid (adipose tissue, liver, brain) synthesis from pyruvate (By similarity).
Gene Name:
PC
Uniprot ID:
Q29RK2
Molecular weight:
129698.0
Reactions
Propionyl-CoA + Adenosine triphosphate + Hydrogen carbonate → S-Methylmalonyl-CoA + ADP + Hydrogen phosphatedetails
Propionyl-CoA + Hydrogen carbonate + Adenosine triphosphate → S-Methylmalonyl-CoA + ADP + Hydrogendetails