MolNFT v1 · #69420 · protein
Crystal structure of a novel vitamin D3 analogue, ZK203278 showing dissociated profile
3KPZ · Vitamin D3 receptor: “Crystal structure of a novel vitamin D3 analogue, ZK203278 showing dissociated profile”. X-ray diffraction, 1 ligand (ZNE), 2 pockets (best druggability 0.86). MolNFT v1 #69420 on GenesisL1: 3D structure…
- PDB
- 3KPZ
- Type
- protein
- Length
- 253 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor
- UniProt
- P11473
- Ligands
- ZNE
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 253 | 67% helix, 3% strand | P11473 |
Ligands and binding sites
- ZNE · (1R,3S,5Z)-5-[(2E)-2-{(1R,3aS,7aR)-1-[(1R,5S)-5-hydroxy-1-methyl-5-(1,3-thiazol-2-yl)pentyl]-7a-methyloctahydro-4H-inden-4-ylidene}ethylidene]-4-methylidenecyclohexane-1,3-diol · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.86 | 0.95 | 36 | ZNE |
| 2 | 67 | 0.32 | 0.75 | 18 | empty |
Compared structures
- 3KPZ · Crystal structure of a novel vitamin D3 analogue, ZK203278 showing dissociated profile · 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 3KPZ · PDBe 3KPZ · UniProt P11473
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