MolNFT v1 · #82891 · protein

Crystal structure analysis of vitamin D receptor

3W0Y · Vitamin D3 receptor: “Crystal structure analysis of vitamin D receptor”. X-ray diffraction, 1 ligand (DS4), 2 pockets (best druggability 0.86). MolNFT v1 #82891 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3W0Y
Type: protein
Length: 250 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vitamin D3 receptor
UniProt: P11473
Ligands: DS4
Pockets: 2 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 66% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vitamin D3 receptor	protein	250	66% helix, 3% strand	P11473

Ligands and binding sites

DS4 · [3-fluoro-2'-methyl-4'-(3-{3-methyl-4-[(1E)-4,4,4-trifluoro-3-hydroxy-3-(trifluoromethyl)but-1-en-1-yl]phenyl}pentan-3-yl)biphenyl-4-yl]acetic acid · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	318	0.86	0.95	37	DS4
2	68	0.30	0.74	14	empty

Compared structures

3W0Y · Crystal Structure Analysis of Vitamin D receptor · the same entry in another collection · chain A against A, TM-score 1.00
P11473 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor (P11473) · a predicted model of the same protein · chain A against A, TM-score 0.95

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P11473
Elsewhere: RCSB PDB 3W0Y · PDBe 3W0Y · UniProt P11473

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