P. aeruginosa Metabolome Database: coenzyme B<sub>12</sub> (PAMDB110425)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB110425

Identification

Name:

coenzyme B₁₂

Description:

A member of the class of cobalamins that is vitamin B₁₂ in which the cyano group is replaced by a 5'-deoxyadenos-5'-yl moiety. It is one of the two metabolically active form of vitamin B₁₂.

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

adenosylcobalamin
cobamide coenzyme
deoxyadenosylcobalamin
cobamamide
vitamin B₁₂
cobamamid
5,6-dimethylbenzimidazolyl-5-deoxyadenosyl-cobamide
(5'-deoxy-5'-adenosyl)cobamide coenzyme
(5,6-dimethylbenzimidazolyl)cobamide coenzyme
5'-deoxy-5'-adenosylcobalamin
5'-deoxyadenosyl vitamin B12
5'-deoxyadenosyl-5,6-dimethylbenzimidazolylcobamide
5'-deoxyadenosylcobalamin
5,6-dimethylbenzimidazolyl-Co-5'-deoxyadenosylcobamide
calomide
cobalamin coenzyme
dibencozide
funacomide

Chemical Formula:

C₇₂H₁₀₀N₁₈O₁₇PCo

Average Molecular Weight:

1579.6

Monoisotopic Molecular Weight:

1579.6661706214

InChI Key:

ZIHHMGTYZOSFRC-YGHJOQEPSA-L

InChI:

InChI=1S/C62H90N13O14P.C10H12N5O3.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);2-4,6-7,10,16-17H,1H2,(H2,11,12,13);/q;;+2/p-2/t31-,34+,35+,36+,37-,41+,52+,53+,56+,57-,59-,60-,61-,62-;4-,6-,7-,10-;/m01./s1

CAS number:

13870-90-1

IUPAC Name:

Coα-[α-(5,6-dimethylbenzimidazolyl)]-Coβ-(5'-deoxy-5'-adenosyl)cobamide

Traditional IUPAC Name:

Not Available

SMILES:

CC%15(C=C%13(C(N%12(C%14(OC(CO)C(OP([O-])(=O)OC(C)CNC(=O)CCC1(C(CC(N)=O)C2(C4(C)(C(C)(CC(N)=O)C(CCC(=O)N)C3(C(C)=C6(C(CC(=O)N)(C(CCC(N)=O)C5(C=C8(C(C)(C)C(CCC(N)=O)C7(C(C)=C1N2[Co---]([N+]=34)([N+]=56)([N+]=78)(CC9(C(C(O)C(O9)N%10(C=NC%11(C%10=NC=NC=%11N)))O))[N+](=C%12)%13))))C)))))(C))C(O)%14)))=CC(C)=%15))

Chemical Taxonomy

Taxonomy Description

This compound belongs to the class of organic compounds known as cobalamin derivatives. These are organic compounds containing a corrin ring, a cobalt atom, an a nucleotide moiety. Cobalamin Derivatives are actually derived from vitamin B12.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Corrinoids

Direct Parent

Cobalamin derivatives

Alternative Parents

Substituents

Cobalamin
Metallotetrapyrrole skeleton
Pentose phosphate
5'-deoxyribonucleoside
Glycosyl compound
N-glycosyl compound
6-aminopurine
Monosaccharide phosphate
Pentose monosaccharide
Purine
Imidazopyrimidine
Benzimidazole
Aminopyrimidine
Organic phosphoric acid derivative
Pyrimidine
N-substituted imidazole
Monosaccharide
Benzenoid
Fatty amide
Imidolactam
Fatty acyl
Azole
Pyrroline
Imidazole
Heteroaromatic compound
Pyrrolidine
Tetrahydrofuran
Amino acid or derivatives
Carboxamide group
Lactam
Secondary carboxylic acid amide
Secondary alcohol
Primary carboxylic acid amide
Organic transition metal salt
Azacycle
Carboxylic acid derivative
Organic metal salt
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Oxacycle
Metalloheterocycle
Primary amine
Transition metal alkyl
Organic zwitterion
Alcohol
Organopnictogen compound
Organic oxygen compound
Hydrocarbon derivative
Organic nitrogen compound
Organic transition metal moeity
Carbonyl group
Organic salt
Organometallic compound
Organonitrogen compound
Organooxygen compound
Organic oxide
Amine
Primary alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

a vitamin B\u003csub\u003e12\u003c/sub\u003e (ADENOSYLCOBALAMIN)

Physical Properties

State:

Solid

Charge:

Melting point:

Not Available

Experimental Properties:

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	0.069 mg/mL	ALOGPS
logP	0.37	ALOGPS
logS	-4.4	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	598.55 Å²	ChemAxon
Rotatable Bond Count	19	ChemAxon
Refractivity	408.83 m³·mol^-1	ChemAxon
Polarizability	158.83 Å³	ChemAxon
Number of Rings	15	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Not Available

Reactions:

ATP + cob(I)alamin → coenzyme B12 + Triphosphate

Pathways:

Propanoate Metabolism pae00640
Valine, Leucine and Isoleucine Degradation pae00280

Spectra

Spectra:

Not Available

References

References:

Tang KH, Harms A, Frey PA (2002)Identification of a novel pyridoxal 5'-phosphate binding site in adenosylcobalamin-dependent lysine 5,6-aminomutase from Porphyromonas gingivalis. Biochemistry 41, Pubmed: 12093296
Moras E, Hosack A, Watkins D, Rosenblatt DS (2007)Mitochondrial vitamin B12-binding proteins in patients with inborn errors of cobalamin metabolism. Molecular genetics and metabolism 90, Pubmed: 17011224
Cole AG, Yoder LM, Shiang JJ, Anderson NA, Walker LA, Banaszak Holl MM, Sension RJ (2002)Time-resolved spectroscopic studies of B(12) coenzymes: a comparison of the primary photolysis mechanism in methyl-, ethyl-, n-propyl-, and 5'-deoxyadenosylcobalamin. Journal of the American Chemical Society 124, Pubmed: 11792214

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Download (PDF)

Links

External Links:

Resource	Link
CAS	13870-90-1
ChEBI	18408
HMDB	HMDB02086
IAF1260	34204
KEGG	C00194
MetaboLights	MTBLC18408
PubChem	46926217

coenzyme B12 (PAMDB110425)

Structure for coenzyme B12 (PAMDB110425)

coenzyme B₁₂ (PAMDB110425)

Structure for coenzyme B₁₂ (PAMDB110425)