Adenosyl cobinamide (ECMDB06903) (M2MDB000706)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (3)XML
Proteins (848)
Record Information
Version2.0
Creation Date2012-05-31 14:10:15 -0600
Update Date2015-09-17 15:41:23 -0600
Secondary Accession Numbers
  • ECMDB06903
Identification
Name:Adenosyl cobinamide
DescriptionAdenosyl cobinamide is an intermediate in Porphyrin and chlorophyll metabolism. It is the third to last step in the synthesis of vitamin B12 coenzyme and is converted from adenosyl cobyrinate hexaamide via the enzyme cobalamin biosynthetic protein CobC. It is then converted to adenosyl cobinamide phosphate via the enzyme adenosylcobinamide kinase / adenosylcobinamide-phosphate guanylyltransferase [EC:2.7.1.156 and EC 2.7.7.62].
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 5'-Deoxy-5'-adenosylcobinamide
  • Adenosylcobinamide
Chemical Formula:C58H84CoN16O11
Weight:Average: 1240.3214
Monoisotopic: 1239.583747804
InChI Key:PAUPKJHCFVPREX-VUCSARQQSA-M
InChI:InChI=1S/C48H73N11O8.C10H12N5O3.Co/c1-23(60)22-55-38(67)16-17-45(6)29(18-35(52)64)43-48(9)47(8,21-37(54)66)28(12-15-34(51)63)40(59-48)25(3)42-46(7,20-36(53)65)26(10-13-32(49)61)30(56-42)19-31-44(4,5)27(11-14-33(50)62)39(57-31)24(2)41(45)58-43;1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15;/h19,23,26-29,43,60H,10-18,20-22H2,1-9H3,(H14,49,50,51,52,53,54,55,56,57,58,59,61,62,63,64,65,66,67);2-4,6-7,10,16-17H,1H2,(H2,11,12,13);/q;;+3/p-1/t23-,26-,27-,28-,29+,43-,45-,46+,47+,48+;;/m1../s1
CAS number:Not Available
IUPAC Name:(3R,4S,5S,9S,10S,15S,19R,20R,21R)-1-{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}-5,10,15-tris(2-carbamoylethyl)-4,9,20-tris(carbamoylmethyl)-19-(2-{[(2R)-2-hydroxypropyl]carbamoyl}ethyl)-3,4,7,9,14,14,17,19-octamethyl-2lambda5,22,23lambda5,24lambda5-tetraaza-1-cobaltaoctacyclo[11.9.1.1^{1,8}.0^{2,6}.0^{3,21}.0^{16,23}.0^{18,22}.0^{11,24}]tetracosa-2(6),7,11(24),12,16(23),17-hexaene-2,23,24-tris(ylium)-1,1-diuide
Traditional IUPAC Name:(3R,4S,5S,9S,10S,15S,19R,20R,21R)-1-{[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}-5,10,15-tris(2-carbamoylethyl)-4,9,20-tris(carbamoylmethyl)-19-(2-{[(2R)-2-hydroxypropyl]carbamoyl}ethyl)-3,4,7,9,14,14,17,19-octamethyl-2lambda5,22,23lambda5,24lambda5-tetraaza-1-cobaltaoctacyclo[11.9.1.1^{1,8}.0^{2,6}.0^{3,21}.0^{16,23}.0^{18,22}.0^{11,24}]tetracosa-2(6),7,11(24),12,16(23),17-hexaene-2,23,24-tris(ylium)-1,1-diuide
SMILES:C[C@@H](O)CNC(=O)CC[C@]1(C)[C@@H](CC(=O)N)[C@@]2([H])N([Co++]CC3OC(C(O)C3O)N3C=NC4=C3N=CN=C4N)\C1=C(C)/C1=N/C(=C\C3=N\C(=C(C)/C4=N[C@]2(C)[C@@](C)(CC(=O)N)[C@@H]4CCC(=O)N)\[C@@](C)(CC(=O)N)[C@@H]3CCC(=O)N)/C(C)(C)[C@@H]1CCC(=O)N
Chemical Taxonomy
Description belongs to the class of organic compounds known as phenylpyruvic acid derivatives. Phenylpyruvic acid derivatives are compounds containing a phenylpyruvic acid moiety, which consists of a phenyl group substituted at the second position by an pyruvic acid.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassPhenylpyruvic acid derivatives
Direct ParentPhenylpyruvic acid derivatives
Alternative Parents
Substituents
  • Cinnamic acid
  • Cinnamic acid or derivatives
  • Coumaric acid
  • Coumaric acid or derivatives
  • Hydroxycinnamic acid
  • Hydroxycinnamic acid or derivatives
  • Enol-phenylpyruvate
  • Phenol
  • 1-hydroxy-2-unsubstituted benzenoid
  • Monocarboxylic acid or derivatives
  • Enol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carbonyl group
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:1
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.0064 g/LALOGPS
logP-0.28ALOGPS
logP-14ChemAxon
logS-5.3ALOGPS
pKa (Strongest Acidic)12.49ChemAxon
pKa (Strongest Basic)3.92ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count16ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area439.45 ŲChemAxon
Rotatable Bond Count23ChemAxon
Refractivity319.33 m³·mol⁻¹ChemAxon
Polarizability127.45 ųChemAxon
Number of Rings11ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Adenosine triphosphate + Cobinamide + Hydrogen ion <> Adenosyl cobinamide + Triphosphate
Adenosyl cobinamide + Adenosine triphosphate > Adenosyl cobinamide phosphate + ADP + Hydrogen ion
Adenosyl cobinamide + Adenosine triphosphate <> Adenosyl cobinamide phosphate + ADP
Adenosyl cobinamide + Guanosine triphosphate <> Adenosyl cobinamide phosphate + Guanosine diphosphate
Adenosine triphosphate + Cobinamide <> Triphosphate + Adenosyl cobinamide
Cob(I)yrinate a,c diamide + Adenosine triphosphate > Adenosyl cobinamide + Triphosphate
Adenosine triphosphate + Cobinamide > Triphosphate + Adenosyl cobinamide
ATP or GTP + Adenosyl cobinamide > adenosylcobinamide phosphate + ADP or GDP
Adenosine triphosphate + Cob(I)yrinate a,c diamide + Cobinamide <> Triphosphate + Adenosyl cobyrinate a,c diamide + Adenosyl cobinamide
Adenosine triphosphate + Guanosine triphosphate + Adenosyl cobinamide <> Adenosyl cobinamide phosphate + ADP + Guanosine diphosphate
Cobinamide + Adenosine triphosphate + Cobinamide > Adenosyl cobinamide + Triphosphate + Adenosyl cobinamide + Triphosphate
Adenosyl cobinamide + Adenosine triphosphate + Adenosyl cobinamide > Adenosine diphosphate + Hydrogen ion + adenosylcobinamide phosphate + ADP
Adenosyl cobinamide + Adenosine triphosphate > Adenosyl cobinamide phosphate + ADP + Hydrogen ion
SMPDB Pathways:
adenosylcobalamin salvage from cobinamidePW001884 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0077-1930000000-620634bd2e5512c9aed5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-1920000000-90e111941c0e1263a843View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-3900000001-7eceb21cac8ce60ad0aeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0fk9-0390000000-5d83b669e0d75074ed7dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0gw0-0930000000-05d257b7ab19d0a5015fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9500000000-64bdca7f7ce4dc01c6b4View in MoNA
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
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
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
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • 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)Not Available
External Links:
ResourceLink
CHEBI ID2480
HMDB IDHMDB06903
Pubchem Compound ID23657884
Kegg IDC06508
ChemSpider ID21864727
Wikipedia IDNot Available
BioCyc IDADENOSYLCOBINAMIDE
EcoCyc IDADENOSYLCOBINAMIDE

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. Bifunctional adenosylcobalamin biosynthesis protein cobU
General function:
Involved in nucleotide binding
Specific function:
ATP-dependent phosphorylation of adenosylcobinamide and adds GMP to adenosylcobinamide phosphate
Gene Name:
cobU
Uniprot ID:
P0AE76
Molecular weight:
20164
Reactions
ATP or GTP + adenosylcobinamide = adenosylcobinamide phosphate + ADP or GDP.
GTP + adenosylcobinamide phosphate = diphosphate + adenosylcobinamide-GDP.
Protein Details
3. 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.