Adenosyl cobinamide (PAMDB000706)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000706
Identification
Name: Adenosyl cobinamide
Description:Adenosyl 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
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 5'-Deoxy-5'-adenosylcobinamide
  • Adenosylcobinamide
Chemical Formula: C58H84CoN16O11
Average Molecular Weight: 1240.3214
Monoisotopic Molecular Weight: 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:{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,9,14-tris(2-carbamoylethyl)-3,8,19-tris(carbamoylmethyl)-18-(2-{[(2R)-2-hydroxypropyl]carbamoyl}ethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1?,??1?????1??,???tricosa-5(23),6,10(22),11,15(21),16-hexaen-20-yl]cobaltylium
Traditional IUPAC Name: {[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,9,14-tris(2-carbamoylethyl)-3,8,19-tris(carbamoylmethyl)-18-(2-{[(2R)-2-hydroxypropyl]carbamoyl}ethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1?,??1?????1??,???tricosa-5(23),6,10(22),11,15(21),16-hexaen-20-yl]cobaltylium
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
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as metallotetrapyrroles. These are polycyclic compounds containing a tetrapyrrole skeleton combined with a metal atom.
Kingdom Organic compounds
Super ClassOrganoheterocyclic compounds
Class Tetrapyrroles and derivatives
Sub ClassMetallotetrapyrroles
Direct Parent Metallotetrapyrroles
Alternative Parents
Substituents
  • Metallotetrapyrrole skeleton
  • N-glycosyl compound
  • Glycosyl compound
  • 6-aminopurine
  • Purine
  • Imidazopyrimidine
  • Aminopyrimidine
  • Fatty acyl
  • Imidolactam
  • Pyrimidine
  • Primary aromatic amine
  • N-substituted imidazole
  • Monosaccharide
  • Fatty amide
  • Saccharide
  • Heteroaromatic compound
  • Pyrroline
  • Pyrrolidine
  • Oxolane
  • Imidazole
  • Azole
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Primary carboxylic acid amide
  • Ketimine
  • Carboxamide group
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organic metal salt
  • Carboxylic acid derivative
  • Carboxylic acid amide
  • Hydrocarbon derivative
  • Organic transition metal salt
  • Organic cobalt salt
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organometallic compound
  • Organic transition metal moeity
  • Imine
  • Carbonyl group
  • Amine
  • Alcohol
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular Framework Aromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:4
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.0303 mg/mLALOGPS
logP1.55ALOGPS
logP-5.2ChemAxon
logS-4.6ALOGPS
pKa (Strongest Acidic)12.47ChemAxon
pKa (Strongest Basic)8.76ChemAxon
Physiological Charge4ChemAxon
Hydrogen Acceptor Count19ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area467.5 Å2ChemAxon
Rotatable Bond Count24ChemAxon
Refractivity313.7 m3·mol-1ChemAxon
Polarizability127.2 Å3ChemAxon
Number of Rings8ChemAxon
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 + 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
Pathways:
Spectra
Spectra:
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