Research workbench
Structural basis for the accommodation of bis- and tris-aromatic derivatives in vitamin D nuclear receptor
Analyse Structural basis for the accommodation of bis- and tris-aromatic derivatives in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G1D
- Type
- protein
- Length
- 250 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor a; Nuclear receptor coactivator 1
- UniProt
- Q9PTN2, Q15788
- Ligands
- 0VK
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor a | protein | 239 | 68% helix, 3% strand | Q9PTN2 |
| B | Nuclear receptor coactivator 1 | protein | 11 | 64% helix, 0% strand | Q15788 |
Ligands and binding sites
- 0VK · 3-(5'-{[3,4-bis(hydroxymethyl)benzyl]oxy}-2'-methyl-2-propylbiphenyl-4-yl)pentan-3-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 | 352 | 0.86 | 0.95 | 41 | 0VK |
| 2 | 172 | 0.45 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 583 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4G1D · 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 4G1D · PDBe 4G1D · UniProt Q9PTN2 · UniProt Q15788
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