DB00169 : cholecalciferol

Approved nutraceutical cholecalciferol ... 1 target DB00169

Generic name: cholecalciferol PDB Het Group: VD3
5 structures in PDB
Brand name(s): delsterol, delta-d, deparal, ebivit, micro-dee, oleovitamin d3, provitamin d3, provitamine, provitina, ricketon, trivitan, vigantol, vigorsan.
Formula: C27H44O
IUPAC Formula: (1s,3z)-3-{2-[(1r,3as,4e,7ar)-7a-Methyl-1-[(2r)-6-Methylheptan-2-Yl]-Octahydro-1h-Inden-4-
PDB name: (1s,3z)-3-[(2e)-2-[(1r,3ar,7as)-7a-Methyl-1-[(2r)-6-Methylheptan-2-Yl]-2,3,3a,5,6,7-Hexahydro-1h-

There is 1 target protein defined in DrugBank for this nutraceutical.
The target protein has one or more structures in the PDB.
There are 5 PDB structures containing the nutraceutical molecule bound to a protein that is not specified as a target.
KEGG drug
Ligand Expo


Target proteins

DrugBank nutraceutical Target 1:   UniProt id: P11473 (VDR_HUMAN)  -  Vitamin D3 receptor
UniProt id: P11473    426 a.a.  
1. 1ie9 A     255 a.a. 255   X-ray 1.40 Å
  2. 3a40 X     255 a.a. 255   X-ray 1.45 Å
  3. 3p8x A     255 a.a. 255   X-ray 1.70 Å
  4. 3a3z X     255 a.a. 255   X-ray 1.72 Å
  5. 3a78 A     255 a.a. 255   X-ray 1.90 Å
   more ...
There are no PDB entries containing cholecalciferol bound to this target protein, although there are 42 entries of the target protein (click the orange, plus icon for a list).

Key:    PfamA domain  Secondary structure  Bound drug molecule


Other proteins with cholecalciferol bound in the PDB

There are 3 "non-target" proteins in the PDB containing the cholecalciferol molecule bound. That is, the UniProt code for the proteins is missing or does not match the nutraceutical target above.

Protein 1:   UniProt id: C4B644 ()  -  Vitamin D(3) 25-hydroxylase OS=Pseudonocardia autotrophica GN=vdh PE=1 SV=1
UniProt id: C4B644    402 a.a.  
1. 3vrm A   402 a.a. 401   X-ray 2.57 Å
  2. 3a50 A,B,C,D,E   402 a.a. 398   X-ray 2.05 Å
The PDB contains 2 entries of cholecalciferol bound to this protein
Protein 2:   UniProt id: P02754 ()  -  Beta-lactoglobulin OS=Bos taurus GN=LGB PE=1 SV=3
UniProt id: P02754    177 a.a.  
2gj5 A   161 a.a. 161   X-ray 2.40 Å
The PDB contains 1 entry of cholecalciferol bound to this protein
Protein 3:   UniProt id: Q6VVX0 ()  -  Vitamin D 25-hydroxylase OS=Homo sapiens GN=CYP2R1 PE=1 SV=1
UniProt id: Q6VVX0    500 a.a.  
1. 2ojd A,B   464 a.a. 463   X-ray 2.70 Å
  2. 3c6g A,B   464 a.a. 463   X-ray 2.80 Å
The PDB contains 2 entries of cholecalciferol 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.


Structure selection

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LIGPLOT diagrams
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