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DB00115 : cyanocobalamin

Approved nutraceutical cyanocobalamin ... 6 targets DB00115

Generic name: cyanocobalamin PDB Het Group: CNC
 
11 structures in PDB
Brand name(s): bedoz, berocca pn, berubigen, cobex, cobolin-m, crystamine, cyanoject, cyomin, depinar, neuroforte-r, primabalt, rubivite, rubramin pc, ruvite, shovite, vibal, vitabee 12.
Formula: C63H89Con14O14P
IUPAC Formula: None
PDB name: Co-Cyanocobalamin

6
There are 6 target proteins defined in DrugBank for this nutraceutical.
 5 
5 of these target proteins have one or more structures in the PDB.
 10 
There are 10 PDB structures containing the nutraceutical molecule bound to a protein that is not specified as a target.
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Information  
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Target proteins

DrugBank nutraceutical Target 1:   UniProt id: Q99707 (METH_HUMAN)  -  Methionine synthase
UniProt id: Q99707    1264 a.a.  
1. 4ccz A     611 a.a. 611   X-ray 2.70 Å
  2. 2o2k A,B     332 a.a. 330   X-ray 1.60 Å
There are no PDB entries containing cyanocobalamin bound to this target protein, although there are 2 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 2:   UniProt id: P22033 (MUTA_HUMAN)  -  Methylmalonyl-CoA mutase, mitochondrial
UniProt id: P22033    749 a.a.  
1. 3bic A,B     715 a.a. 713   X-ray 2.60 Å
  2. 2xiq A,B     714 a.a. 712   X-ray 1.95 Å
  3. 2xij A     710 a.a. 708   X-ray 1.95 Å
There are no PDB entries containing cyanocobalamin bound to this target protein, although there are 3 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 3:   UniProt id: Q9UBK8 (MTRR_HUMAN)  -  Methionine synthase reductase, mitochondrial
UniProt id: Q9UBK8    724 a.a.  
1. 2qtz A     445 a.a. 442   X-ray 1.90 Å
  2. 2qtl A     445 a.a. 441   X-ray 1.90 Å
There are no PDB entries containing cyanocobalamin bound to this target protein, although there are 2 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 4:   UniProt id: Q8IVH4 (MMAA_HUMAN)  -  Methylmalonic aciduria type A protein, mitochondrial
UniProt id: Q8IVH4    417 a.a.  
2www A     298 a.a. 298   X-ray 2.64 Å
There are no PDB entries containing cyanocobalamin bound to this target protein, although there is 1 entry of the target protein in the PDB (see above).
DrugBank nutraceutical Target 5:   UniProt id: Q9Y4U1 (MMAC_HUMAN)  -  Methylmalonic aciduria and homocystinuria type C protein
UniProt id: Q9Y4U1    281 a.a.  
1. 3sc0 A     237 a.a. 237   X-ray 1.95 Å
  2. 3sbz A     234 a.a. 234   X-ray 2.00 Å
  3. 3som A,B,C,D,...     227 a.a. 227   X-ray 2.40 Å
  4. 3sby A,B     218 a.a. 213   X-ray 2.71 Å
There are no PDB entries containing cyanocobalamin bound to this target protein, although there are 4 entries of the target protein (click the orange, plus icon for a list).
DrugBank nutraceutical Target 6:   UniProt id: P42898 (MTHR_HUMAN)  -  Methylenetetrahydrofolate reductase
UniProt id: P42898    656 a.a.  
 
There are no structures of the target protein in the PDB (click icon on left for list of closest matches)

Key:    PfamA domain  PfamB domain  Secondary structure  Bound drug molecule

 

Other proteins with cyanocobalamin bound in the PDB

There are 5 "non-target" proteins in the PDB containing the cyanocobalamin molecule bound. That is, the UniProt code for the proteins is missing or does not match any of the nutraceutical targets listed above.

Protein 1:   UniProt id: P06129 ()  -  Vitamin B12 transporter BtuB OS=Escherichia coli (strain K12) GN=btuB PE=1 SV=2
UniProt id: P06129    613 a.a.  
1. 2gsk A   590 a.a. 590   X-ray 2.10 Å
  2. 1nqh A   584 a.a. 584   X-ray 3.10 Å
  3. 3m8d A   583 a.a. 582   X-ray 2.44 Å
The PDB contains 3 entries of cyanocobalamin bound to this protein
Protein 2:   UniProt id: P20061 ()  -  Transcobalamin-1 OS=Homo sapiens GN=TCN1 PE=1 SV=2
UniProt id: P20061    432 a.a.  
4kki A   398 a.a. 397   X-ray 2.35 Å
The PDB contains 1 entry of cyanocobalamin bound to this protein
Protein 3:   UniProt id: P37028 ()  -  Vitamin B12-binding protein OS=Escherichia coli (strain K12) GN=btuF PE=1 SV=2
UniProt id: P37028    265 a.a.  
1. 1n2z A,B   245 a.a. 245   X-ray 2.00 Å
  2. 1n4a A,B   244 a.a. 244   X-ray 2.00 Å
The PDB contains 2 entries of cyanocobalamin bound to this protein
Protein 4:   UniProt id: P80078 ()  -  Glutamate mutase sigma subunit OS=Clostridium cochlearium GN=glmS PE=1 SV=2
UniProt id: P80078    136 a.a.  
1ccw A,C   137 a.a. 134   X-ray 1.60 Å
The PDB contains 1 entry of cyanocobalamin bound to this protein
Protein 5:   UniProt id: Q59470 ()  -  Diol dehydrase alpha subunit OS=Klebsiella oxytoca GN=pddA PE=1 SV=1
UniProt id: Q59470    553 a.a.  
1. 1uc4 A,L   551 a.a. 550   X-ray 1.80 Å
  2. 1egm A,L   551 a.a. 550   X-ray 1.85 Å
  3. 1uc5 A,L   551 a.a. 550   X-ray 2.30 Å
The PDB contains 3 entries of cyanocobalamin bound to this protein

Key:    PfamA domain  Secondary structure  Bound drug molecule

The black crosses on the secondary structure diagrams indicate where the PDB and UniProt sequences differ.

Where there is more than one PDB model for a given UniProt sequence, the models are ordered by: 1. decreasing order of similarity to the UniProt sequence, 2. X-ray structures (in order of increasing resolution), NMR structures, and theoretical models. Clicking on any PDB code take you to the corresponding PDBsum page.

 

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