Adenosylcobinamide-GDP (ECMDB12185) (M2MDB000826)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (444)
Record Information
Version2.0
Creation Date2012-05-31 14:20:55 -0600
Update Date2015-09-17 15:41:47 -0600
Secondary Accession Numbers
  • ECMDB12185
Identification
Name:Adenosylcobinamide-GDP
DescriptionAdenosylcobinamide-GDP,a known de novo intermediate, is involved in Porphyrin and chlorophyll metabolism.In Salmonella typhimurium LT2, under anaerobic conditions, CobU (EC 2.7.7.62 and EC 2.7.1.156), CobT (EC 2.4.2.21), CobC (EC 3.1.3.73) and CobS (EC 2.7.8.26) catalyse reactions in the nucleotide loop
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • Adenosine-GDP-cobinamide
Chemical Formula:C68H97CoN21O21P2
Weight:Average: 1665.5066
Monoisotopic: 1664.597512489
InChI Key:IQTYKHRKNGVJEO-FGHWVWCISA-M
InChI:InChI=1S/C58H86N16O18P2.C10H12N5O3.Co/c1-25(91-94(87,88)92-93(85,86)89-23-33-45(82)46(83)52(90-33)74-24-67-44-50(74)71-53(65)72-51(44)84)22-66-41(81)16-17-55(6)31(18-38(62)78)49-58(9)57(8,21-40(64)80)30(12-15-37(61)77)43(73-58)27(3)48-56(7,20-39(63)79)28(10-13-35(59)75)32(68-48)19-34-54(4,5)29(11-14-36(60)76)42(69-34)26(2)47(55)70-49;1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15;/h19,24-25,28-31,33,45-46,49,52,82-83H,10-18,20-23H2,1-9H3,(H19,59,60,61,62,63,64,65,66,68,69,70,71,72,73,75,76,77,78,79,80,81,84,85,86,87,88);2-4,6-7,10,16-17H,1H2,(H2,11,12,13);/q;;+2/p-1/t25?,28-,29-,30-,31+,33-,45-,46-,49?,52-,55-,56+,57+,58+;4-,6-,7-,10-;/m11./s1
CAS number:Not Available
IUPAC Name:(3R,4S,5S,9S,10S,15S,19R,20R,21R)-19-(2-{[(2R)-2-({[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)propyl]carbamoyl}ethyl)-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)-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)-19-(2-{[(2R)-2-[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]propyl]carbamoyl}ethyl)-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)-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:CC(CNC(=O)CC[C@]1(C)[C@@H](CC(N)=O)C2N=C1\C(C)=C1/N=C(/C=C3\N=C(\C(\C)=C4\[C@@H](CCC(N)=O)[C@](C)(CC(N)=O)[C@@]2(C)N4[Co+]C[C@H]2O[C@H]([C@H](O)[C@@H]2O)N2C=NC4=C2N=CN=C4N)[C@@](C)(CC(N)=O)[C@@H]3CCC(N)=O)C(C)(C)[C@@H]1CCC(N)=O)OP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=C(N)NC2=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine ribonucleotides
Direct ParentPurine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine ribonucleoside diphosphate
  • Metallotetrapyrrole skeleton
  • Purine ribonucleoside monophosphate
  • Tetrapyrrole skeleton
  • Pentose phosphate
  • Pentose-5-phosphate
  • 5'-deoxyribonucleoside
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • 6-oxopurine
  • Hypoxanthine
  • 6-aminopurine
  • Monosaccharide phosphate
  • Purine
  • Imidazopyrimidine
  • Phosphoethanolamine
  • Monoalkyl phosphate
  • Aminopyrimidine
  • Hydroxypyrimidine
  • Pyrimidone
  • Phosphoric acid ester
  • Fatty amide
  • Fatty acyl
  • Imidolactam
  • Pyrimidine
  • Alkyl phosphate
  • Monosaccharide
  • Organic phosphoric acid derivative
  • N-substituted imidazole
  • Pyrrolidine
  • Pyrroline
  • Vinylogous amide
  • Azole
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Imidazole
  • Primary carboxylic acid amide
  • Secondary alcohol
  • Amino acid or derivatives
  • Secondary carboxylic acid amide
  • Ketimine
  • Carboxamide group
  • Carboximidic acid
  • Carboximidic acid derivative
  • Oxacycle
  • Carboxylic acid derivative
  • Secondary aliphatic amine
  • Enamine
  • Azacycle
  • Organic transition metal salt
  • Organoheterocyclic compound
  • Carbene-type 1,3-dipolar compound
  • Secondary amine
  • Organic oxide
  • Organopnictogen compound
  • Amine
  • Alcohol
  • Hydrocarbon derivative
  • Organic cobalt salt
  • Carbonyl group
  • Organic salt
  • Organic nitrogen compound
  • Imine
  • Organic oxygen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular FrameworkNot Available
External Descriptors
Physical Properties
State:Solid
Charge:-1
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.033 g/LALOGPS
logP0.07ALOGPS
logP-16ChemAxon
logS-4.7ALOGPS
pKa (Strongest Acidic)1.85ChemAxon
pKa (Strongest Basic)4.01ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count26ChemAxon
Hydrogen Donor Count16ChemAxon
Polar Surface Area656.5 ŲChemAxon
Rotatable Bond Count31ChemAxon
Refractivity401.91 m³·mol⁻¹ChemAxon
Polarizability161.78 ųChemAxon
Number of Rings14ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Adenosylcobinamide-GDP + N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole > Adenosylcobalamin + Guanosine monophosphate + Hydrogen ion
Adenosyl cobinamide phosphate + Guanosine triphosphate + Hydrogen ion > Adenosylcobinamide-GDP + Pyrophosphate
Adenosyl cobinamide phosphate + Guanosine triphosphate <> Adenosylcobinamide-GDP + Pyrophosphate
Adenosylcobalamin + Guanosine monophosphate <> Adenosylcobinamide-GDP + N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole
Adenosylcobinamide-GDP + N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole > adenosylcobalamin 5'-phosphate + Guanosine monophosphate + Hydrogen ion
Adenosylcobinamide-GDP + N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole Hydrogen ion + Adenosylcobalamin + Guanosine monophosphate
Guanosine triphosphate + adenosylcobinamide phosphate > Pyrophosphate + Adenosylcobinamide-GDP
Adenosylcobinamide-GDP + N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole + N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole <> Guanosine monophosphate + Adenosylcobalamin + Adenosylcobalamin 5'-phosphate
adenosylcobinamide phosphate + Guanosine triphosphate + Hydrogen ion > Pyrophosphate + Adenosylcobinamide-GDP + Adenosylcobinamide-GDP
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole + Adenosylcobinamide-GDP + Adenosylcobinamide-GDP > Hydrogen ion + GMP + Adenosylcobalamin 5'-phosphate
Adenosyl cobinamide phosphate + Guanosine triphosphate + Hydrogen ion > Adenosylcobinamide-GDP + Pyrophosphate
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, Positivesplash10-0udi-0900004000-b99417703a97697aab48View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0820029000-f0beaa26df346053a517View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-0930000000-ef31295f338a08f3c804View 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
  • 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 ID2479
HMDB IDHMDB12185
Pubchem Compound ID23724503
Kegg IDC06510
ChemSpider ID29368592
Wikipedia IDNot Available
BioCyc IDADENOSYLCOBINAMIDE-GDP
EcoCyc IDADENOSYLCOBINAMIDE-GDP

Enzymes

Protein Details
1. 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
2. Cobalamin synthase
General function:
Involved in cobalamin 5'-phosphate synthase activity
Specific function:
Joins Ado-cobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin)
Gene Name:
cobS
Uniprot ID:
P36561
Molecular weight:
26385
Reactions
GDP-cobinamide + alpha-ribazole = cobalamin + GMP.