ChemFOnt: Showing chemical card for Adenosyl cobinamide (CFc000003003)

Record Information

Version

1.0

Creation Date

2022-08-28 10:25:12 UTC

Update Date

2022-09-13 18:48:01 UTC

Chemfont ID

CFc000003003

Molecule Identification

Common Name

Adenosyl cobinamide

Definition

Adenosyl cobinamide is an intermediate in vitamin B12 cofactor biosynthesis and adenosylcobalamin synthesis. It is a substrate for the enzyme Cob(I)yrinic acid a,c-diamide adenosyltransferase which is found in the mitochondria. The enzyme is responsible for the following 2 step reaction: ATP + cob(I)yrinic acid a,c-diamide = triphosphate + adenosylcob(III)yrinic acid a,c-diamide and then ATP + cobinamide = triphosphate + adenosylcobinamide.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
5'-Deoxy-5'-adenosylcobinamide	HMDB
Adenosylcobinamide	HMDB

Chemical Formula

C₅₈H₈₄CoN₁₆O₁₁

Average Molecular Weight

1240.3214

Monoisotopic Molecular Weight

1239.583747804

IUPAC Name

cobalt(3+) ion 3-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,14-bis[2-(C-hydroxycarbonimidoyl)ethyl]-3,8,19-tris[(C-hydroxycarbonimidoyl)methyl]-18-(2-{[(2R)-2-hydroxypropyl]-C-hydroxycarbonimidoyl}ethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-9-yl]propan-1-aminide [5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl

Traditional Name

cobalt(3+) ion 3-[(1R,2R,3S,4S,8S,9S,14S,18R,19R)-4,14-bis[2-(C-hydroxycarbonimidoyl)ethyl]-3,8,19-tris(C-hydroxycarbonimidoylmethyl)-18-(2-{[(2R)-2-hydroxypropyl]-C-hydroxycarbonimidoyl}ethyl)-2,3,6,8,13,13,16,18-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5,7(22),10,12(21),15,17(20)-hexaen-9-yl]propan-1-aminide [5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl

CAS Registry Number

None

SMILES

[Co+3].[CH2]C1OC(C(O)C1O)N1C=NC2=C(N)N=CN=C12.[H][C@](C)(O)CN=C(O)CC[C@@]1(C)C2=N[C@]([H])([C@]1([H])CC(O)=N)[C@]1(C)NC(=C(C)C3=NC(=CC4=NC(=C2C)[C@@]([H])(CCC(O)=N)C4(C)C)[C@@]([H])(CCC([NH-])=O)[C@]3(C)CC(O)=N)[C@@]([H])(CCC(O)=N)[C@]1(C)CC(O)=N

InChI Identifier

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

InChI Key

PAUPKJHCFVPREX-VUCSARQQSA-M

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.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Metallotetrapyrroles

Direct Parent

Metallotetrapyrroles

Alternative Parents

Substituents

Metallotetrapyrrole skeleton
5'-deoxyribonucleoside
Glycosyl compound
N-glycosyl compound
6-aminopurine
Pentose monosaccharide
Imidazopyrimidine
Purine
Aminopyrimidine
Fatty amide
Monosaccharide
N-substituted imidazole
Pyrimidine
Imidolactam
Fatty acyl
Azole
Tetrahydrofuran
Pyrroline
Pyrrolidine
Imidazole
Heteroaromatic compound
Carboxamide group
Secondary carboxylic acid amide
Secondary alcohol
Amino acid or derivatives
Primary carboxylic acid amide
Ketimine
Azacycle
Organic metal salt
Organic transition metal salt
Carboxylic acid derivative
Oxacycle
Organooxygen compound
Organonitrogen compound
Alcohol
Hydrocarbon derivative
Primary amine
Imine
Organic oxide
Transition metal alkyl
Organopnictogen compound
Organic nitrogen compound
Organic cobalt salt
Carbonyl group
Organic salt
Organic oxygen compound
Amine
Organic transition metal moeity
Organometallic compound
Organic cation
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0006903)
Membrane (HMDB: HMDB0006903)

Source

Exogenous

Exogenous (HMDB: HMDB0006903)

Food

Animal origin

Poultry

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Endogenous

Endogenous (HMDB: HMDB0006903)

Process

Naturally occurring process

Biological process

Biochemical pathway

Metabolic pathway

Adenosylcobalamin Salvage from Cobinamide (PathBank: SMP0122099)

Role

Not Available

Physical Properties

Predicted Properties

Property	Value	Source
Water Solubility	0.027 g/L	ALOGPS
logP	2.73	ALOGPS
logP	-2.6	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	4.97	ChemAxon
pKa (Strongest Basic)	9.07	ChemAxon
Physiological Charge	3	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	14	ChemAxon
Polar Surface Area	359.63 Å²	ChemAxon
Rotatable Bond Count	21	ChemAxon
Refractivity	308.41 m³·mol⁻¹	ChemAxon
Polarizability	100.62 Å³	ChemAxon
Number of Rings	8	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB024150

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

Showing chemical card for Adenosyl cobinamide (CFc000003003)

MOL for CFc000003003 (Adenosyl cobinamide)

3D MOL for CFc000003003 (Adenosyl cobinamide)

3D SDF for CFc000003003 (Adenosyl cobinamide)

3D-SDF for CFc000003003 (Adenosyl cobinamide)

PDB for CFc000003003 (Adenosyl cobinamide)

3D PDB for CFc000003003 (Adenosyl cobinamide)

SMILES for CFc000003003 (Adenosyl cobinamide)

INCHI for CFc000003003 (Adenosyl cobinamide)

Structure for CFc000003003 (Adenosyl cobinamide)

3D Structure for CFc000003003 (Adenosyl cobinamide)