Research workbench
Allene-based design of a noncalcemic vitamin D receptor agonist
Analyse Allene-based design of a noncalcemic vitamin D receptor agonist in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B39
- Type
- protein
- Length
- 251 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
- T0H
- Pockets
- 3 · 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 | 240 | 68% helix, 3% strand | Q9PTN2 |
| B | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 11 | 64% helix, 0% strand | Q15788 |
Ligands and binding sites
- T0H · (1R,3S,Z)-5-(2-((3aS,7aS,E)-1-(6-hydroxy-6-methylhept-1-en-1-ylidene)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-4-methylenecyclohexane-1,3-diol · ligand · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.86 | 0.95 | 38 | T0H, ACT |
| 2 | 225 | 0.55 | 0.78 | 30 | empty |
| 3 | 63 | 0.33 | 0.76 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 644 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
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 7B39 · PDBe 7B39 · UniProt Q9PTN2 · UniProt Q15788
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