Cob(I)yrinate a,c diamide (ECMDB01083) (M2MDB000247)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (327)
Record Information
Version2.0
Creation Date2012-05-31 13:44:51 -0600
Update Date2015-09-17 16:24:05 -0600
Secondary Accession Numbers
  • ECMDB01083
Identification
Name:Cob(I)yrinate a,c diamide
DescriptionCob(I)yrinate a,c diamide is an intermediate in porphyrin and chlorophyll metabolism. It is the sixth to last step in the synthesis of vitamin B12 coenzyme and is converted from Cob(II)yrinate a,c diamide via the enzyme cob(II)yrinic acid a,c-diamide reductase [EC:1.16.8.1]. It is then converted to adenosyl cobyrinate a,c diamide via the enzyme cob(I)alamin adenosyltransferase [EC:2.5.1.17]. Ubiquinone (also known as coenzyme Q) is an isoprenoid quinone that functions as an electron carrier in membranes. Ubiquinone synthesis involves the conversion of chorismate to 4-hydroxybenzoate by choris
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • Cbi
  • Cob(I)yrinate a,c-diamide
  • Cob(I)yrinate diamide
  • Cob(I)yrinic acid a,c diamide
  • Cob(I)yrinic acid a,c-diamide
  • Cob(I)yrinic acid diamide
  • Cobyrinate a,c-diamide
  • Cobyrinic acid a,c-diamide
Chemical Formula:C45H61CoN6O12
Weight:Average: 936.932
Monoisotopic: 936.36794664
InChI Key:NKLHEMWEQJCPPF-OKJGWHJPSA-M
InChI:InChI=1S/C45H62N6O12.Co/c1-21-36-24(10-13-32(56)57)41(3,4)28(49-36)18-27-23(9-12-31(54)55)43(6,19-29(46)52)39(48-27)22(2)37-25(11-14-33(58)59)44(7,20-30(47)53)45(8,51-37)40-26(17-35(62)63)42(5,38(21)50-40)16-15-34(60)61;/h18,23-26,40H,9-17,19-20H2,1-8H3,(H10,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63);/q;+1/p-1/t23-,24-,25-,26+,40-,42-,43+,44+,45+;/m1./s1
CAS number:Not Available
IUPAC Name:λ¹-cobalt(1+) ion 2-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,9,14,18-tetrakis(2-carboxyethyl)-19-(carboxymethyl)-3-[(C-hydroxycarbonimidoyl)methyl]-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-8-yl]ethan-1-aminide
Traditional IUPAC Name:λ¹-cobalt(1+) ion 2-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,9,14,18-tetrakis(2-carboxyethyl)-19-(carboxymethyl)-3-(C-hydroxycarbonimidoylmethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-8-yl]ethanaminide
SMILES:[Co]N1\C2=C(C)/C3=N/C(=C\C4=N\C(=C(C)/C5=N[C@@](C)([C@@]1([H])[C@H](CC(=O)O)[C@@]2(C)CCC(=O)O)[C@@](C)(CC(=O)N)[C@@H]5CCC(=O)O)\[C@@](C)(CC(=O)N)[C@@H]4CCC(=O)O)/C(C)(C)[C@@H]3CCC(=O)O
Chemical Taxonomy
Description belongs to the class of organic compounds known as metallotetrapyrroles. These are polycyclic compounds containing a tetrapyrrole skeleton combined with a metal atom.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassTetrapyrroles and derivatives
Sub ClassMetallotetrapyrroles
Direct ParentMetallotetrapyrroles
Alternative Parents
Substituents
  • Metallotetrapyrrole skeleton
  • Pentacarboxylic acid or derivatives
  • Delta amino acid or derivatives
  • Pyrroline
  • Pyrrolidine
  • Amino acid
  • Ketimine
  • Amino acid or derivatives
  • Azacycle
  • Organic transition metal salt
  • Organic 1,3-dipolar compound
  • Carbene-type 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Secondary amine
  • Enamine
  • Secondary aliphatic amine
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carboximidic acid derivative
  • Carboximidic acid
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic cobalt salt
  • Organic salt
  • Organic zwitterion
  • Organooxygen compound
  • Organonitrogen compound
  • Imine
  • Carbonyl group
  • Amine
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.057 g/LALOGPS
logP0.83ALOGPS
logP-2.8ChemAxon
logS-4.2ALOGPS
pKa (Strongest Acidic)3.52ChemAxon
pKa (Strongest Basic)8.94ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count18ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area316.99 ŲChemAxon
Rotatable Bond Count18ChemAxon
Refractivity239.43 m³·mol⁻¹ChemAxon
Polarizability91.71 ųChemAxon
Number of Rings5ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Cob(I)yrinate a,c diamide + Adenosine triphosphate <> Adenosyl cobyrinate a,c diamide + Triphosphate
Cob(I)yrinate a,c diamide + Adenosine triphosphate > Adenosyl cobinamide + Triphosphate
Adenosine triphosphate + Cob(I)yrinate a,c diamide > Triphosphate + Adenosylcob(III)yrinic acid a,c-diamide
Adenosine triphosphate + Cob(I)yrinate a,c diamide + Cobinamide <> Triphosphate + Adenosyl cobyrinate a,c diamide + Adenosyl cobinamide
SMPDB Pathways:Not Available
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0006-0000000092-26e3d88627f2ca94c1eaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-0000000091-55945455cd80766a0873View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01r6-0000000290-c61187a4621fccf83fccView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0aor-0000000090-3794f8e7f38135f98667View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-066u-0000000090-ff2dfaf3df8ac52acca5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00kf-4000000190-74ca73af45f6760a5be8View 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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID28531
HMDB IDHMDB06904
Pubchem Compound IDNot Available
Kegg IDC06505
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDCOBINAMIDE
EcoCyc IDCOBINAMIDE

Enzymes

Protein Details
1. Cob(I)yrinic acid a,c-diamide adenosyltransferase
General function:
Involved in ATP binding
Specific function:
Required for both de novo synthesis of the corrin ring for the assimilation of exogenous corrinoids. Participates in the adenosylation of a variety of incomplete and complete corrinoids
Gene Name:
btuR
Uniprot ID:
P0A9H5
Molecular weight:
21999
Reactions
ATP + cob(I)yrinic acid a,c-diamide = triphosphate + adenosylcob(III)yrinic acid a,c-diamide.
ATP + cobinamide = triphosphate + adenosylcobinamide.
Protein Details
2. Ethanolamine utilization cobalamin adenosyltransferase
General function:
Involved in ATP binding
Specific function:
Converts CNB12 to ADOB12
Gene Name:
eutT
Uniprot ID:
P65643
Molecular weight:
30171
Reactions
ATP + cob(I)yrinic acid a,c-diamide = triphosphate + adenosylcob(III)yrinic acid a,c-diamide.
ATP + cobinamide = triphosphate + adenosylcobinamide.