MolNFT v1 · #189684 · protein
Vitamin D receptor complexed with a lithocholic acid derivative
7VQP · Vitamin D3 receptor: “Vitamin D receptor complexed with a lithocholic acid derivative”. X-ray diffraction, 1 ligand (7SW), 2 pockets (best druggability 0.83). MolNFT v1 #189684 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7VQP
- Type
- protein
- Length
- 241 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor; Mediator of RNA polymerase II transcription subunit 1
- UniProt
- Q15648
- Ligands
- 7SW
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 231 | 69% helix, 3% strand | — |
| C | Mediator of RNA polymerase II transcription subunit 1 | protein | 10 | 70% helix, 0% strand | Q15648 |
Ligands and binding sites
- 7SW · 3-((R)-4-((3R,5R,8R,9S,10S,13R,14S,17R)-3-(2-hydroxy-2-methylpropyl)-10,13-dimethylhexadecahydro-1H-cyclopenta[a]phenanthren-17-yl)pentanamido)propanoic 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.83 | 0.90 | 39 | 7SW |
| 2 | 61 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 543 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7VQP · Vitamin D receptor complexed with a lithocholic acid derivative · the same entry in another collection · chain A against A, TM-score 1.00
- Q15648 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain C against A, TM-score 0.81
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 Q15648
- Elsewhere: RCSB PDB 7VQP · PDBe 7VQP · UniProt Q15648
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