MolNFT v1 · #92272 · protein
Structural basis for the accommodation of bis- and tris-aromatic derivatives in vitamin D nuclear receptor
4G2H · Vitamin D3 receptor a: “Structural basis for the accommodation of bis- and tris-aromatic derivatives in vitamin D nuclear receptor”. X-ray diffraction, 1 ligand (0VQ), 2 pockets (best druggability 0.86). MolNFT v1 #92272 on…
- PDB
- 4G2H
- Type
- protein
- Length
- 249 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor a; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- Q9PTN2, Q15788
- Ligands
- 0VQ
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor a | protein | 239 | 67% helix, 3% strand | Q9PTN2 |
| B | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 10 | 70% helix, 0% strand | Q15788 |
Ligands and binding sites
- 0VQ · (3E,5E)-6-(3-{2-[3,4-bis(hydroxymethyl)phenyl]ethyl}phenyl)-1,1,1-trifluoro-2-(trifluoromethyl)octa-3,5-dien-2-ol · 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 | 301 | 0.86 | 0.96 | 36 | 0VQ |
| 2 | 162 | 0.44 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 564 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4G2H · Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9PTN2 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor a (Q9PTN2) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9PTN2
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 4G2H · PDBe 4G2H · UniProt Q9PTN2 · UniProt Q15788
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