malonyl-CoA methyl ester (ECMDB23166) (M2MDB003556)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (3)XML
Proteins (851)
Record Information
Version2.0
Creation Date2012-10-10 12:20:05 -0600
Update Date2015-06-03 17:26:04 -0600
Secondary Accession Numbers
  • ECMDB23166
Identification
Name:malonyl-CoA methyl ester
DescriptionMalonyl-CoA methyl ester is an intermediate in biotin synthesis. It a substrate for the enzyme Malonyl-CoA O-methyltransferase BioC which onverts the free carboxyl group of a malonyl-thioester to its methyl ester by transfer of a methyl group from S-adenosyl-L-methionine (SAM). It allows to synthesize pimeloyl-ACP via the fatty acid synthetic pathway. E.coli employs a methylation and demethylation strategy to allow elongation of a temporarily disguised malonate moiety to a pimelate moiety by the fatty acid synthetic enzymes.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • Methyl 3-2-3-(2R)-4-(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-ylmethoxy-hydroxyphosphoryloxy-hydroxyphosphoryloxy-2-hydroxy-3,3-dimethylbutanoylaminopropanoylaminoethylsulfanyl-3-oxopropanoate
  • Methyl 3-2-3-(2R)-4-(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-ylmethoxy-hydroxyphosphoryloxy-hydroxyphosphoryloxy-2-hydroxy-3,3-dimethylbutanoylaminopropanoylaminoethylsulfanyl-3-oxopropanoic acid
  • Methyl 3-2-3-(2R)-4-(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-ylmethoxy-hydroxyphosphoryloxy-hydroxyphosphoryloxy-2-hydroxy-3,3-dimethylbutanoylaminopropanoylaminoethylsulphanyl-3-oxopropanoate
  • Methyl 3-2-3-(2R)-4-(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-ylmethoxy-hydroxyphosphoryloxy-hydroxyphosphoryloxy-2-hydroxy-3,3-dimethylbutanoylaminopropanoylaminoethylsulphanyl-3-oxopropanoic acid
Chemical Formula:C25H40N7O19P3S
Weight:Average: 867.607
Monoisotopic: 867.131252359
InChI Key:CHQAJZULNPRMEN-ITIYDSSPSA-N
InChI:InChI=1S/C25H40N7O19P3S/c1-25(2,20(37)23(38)28-5-4-14(33)27-6-7-55-16(35)8-15(34)46-3)10-48-54(44,45)51-53(42,43)47-9-13-19(50-52(39,40)41)18(36)24(49-13)32-12-31-17-21(26)29-11-30-22(17)32/h11-13,18-20,24,36-37H,4-10H2,1-3H3,(H,27,33)(H,28,38)(H,42,43)(H,44,45)(H2,26,29,30)(H2,39,40,41)/t13-,18-,19-,20+,24-/m1/s1
CAS number:Not Available
IUPAC Name:{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-({[hydroxy({hydroxy[(3R)-3-hydroxy-3-{[2-({2-[(3-methoxy-3-oxopropanoyl)sulfanyl]ethyl}carbamoyl)ethyl]carbamoyl}-2,2-dimethylpropoxy]phosphoryl}oxy)phosphoryl]oxy}methyl)oxolan-3-yl]oxy}phosphonic acid
Traditional IUPAC Name:[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-[({hydroxy[hydroxy(3R)-3-hydroxy-3-{[2-({2-[(3-methoxy-3-oxopropanoyl)sulfanyl]ethyl}carbamoyl)ethyl]carbamoyl}-2,2-dimethylpropoxyphosphoryl]oxyphosphoryl}oxy)methyl]oxolan-3-yl]oxyphosphonic acid
SMILES:COC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N
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
  • Aminopyrimidine
  • Monoalkyl phosphate
  • Organic phosphoric acid derivative
  • N-substituted imidazole
  • N-acyl-amine
  • Phosphoric acid ester
  • Monosaccharide
  • Alkyl phosphate
  • Imidolactam
  • Pyrimidine
  • 1,3-dicarbonyl compound
  • Fatty amide
  • Imidazole
  • Azole
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Methyl ester
  • Carbothioic s-ester
  • Thiocarboxylic acid ester
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Carboxylic acid ester
  • Amino acid or derivatives
  • Thiocarboxylic acid or derivatives
  • Sulfenyl compound
  • Carboxylic acid derivative
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Monocarboxylic acid or derivatives
  • Organic oxygen compound
  • Amine
  • Organonitrogen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Organosulfur compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Primary amine
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-4
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility3.96 g/LALOGPS
logP-0.48ALOGPS
logP-6.9ChemAxon
logS-2.3ALOGPS
pKa (Strongest Acidic)0.83ChemAxon
pKa (Strongest Basic)4.95ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count18ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area389.93 ŲChemAxon
Rotatable Bond Count23ChemAxon
Refractivity183.32 m³·mol⁻¹ChemAxon
Polarizability74.61 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
S-adenosyl-L-methionine + Malonyl-CoA > S-Adenosylhomocysteine + malonyl-CoA methyl ester
SMPDB Pathways:Not Available
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-1911000130-7ec4913dc885ca0c311cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0912000000-27289dd346d4bf2fa94cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-2911000000-d9ea2c85350a03c21b68View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00o0-9821140460-6cd71ffedc1f6bf135fbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-003r-5910010010-ec3af4a8c64ab1635995View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-057i-6900100000-7ce4f36975b302bc9c95View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Yurtsever D. (2007). Fatty acid methyl ester profiling of Enterococcus and Esherichia coli for microbial source tracking. M.sc. Thesis. Villanova University: U.S.A
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound ID46926156
Kegg IDC19673
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. 3-oxoacyl-[acyl-carrier-protein] synthase 1
General function:
Involved in catalytic activity
Specific function:
Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Specific for elongation from C-10 to unsaturated C-16 and C-18 fatty acids
Gene Name:
fabB
Uniprot ID:
P0A953
Molecular weight:
42613
Reactions
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein].
Protein Details
2. 3-oxoacyl-[acyl-carrier-protein] synthase 2
General function:
Involved in transferase activity, transferring acyl groups other than amino-acyl groups
Specific function:
Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Has a preference for short chain acid substrates and may function to supply the octanoic substrates for lipoic acid biosynthesis
Gene Name:
fabF
Uniprot ID:
P0AAI5
Molecular weight:
43045
Reactions
(Z)-hexadec-11-enoyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = (Z)-3-oxooctadec-13-enoyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein].
Protein Details
3. Biotin synthesis protein BioC
General function:
Involved in biotin biosynthetic process
Specific function:
BioC is involved in an early, but chemically unexplored, step in the conversion of pimelic acid to biotin
Gene Name:
bioC
Uniprot ID:
P12999
Molecular weight:
28276
Reactions
S-adenosyl-L-methionine + malonyl-CoA = S-adenosyl-L-homocysteine + malonyl-CoA methyl ester.