MolNFT v1 · #117427 · protein
Potent vitamin D receptor agonist
5E7V · Vitamin D3 receptor a: “Potent vitamin D receptor agonist”. X-ray diffraction, 1 ligand (M7E), 3 pockets (best druggability 0.86). MolNFT v1 #117427 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5E7V
- 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
- UniProt
- Q9PTN2, B5MCN7
- Ligands
- M7E
- 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 | 239 | 68% helix, 3% strand | Q9PTN2 |
| B | Nuclear receptor coactivator 1 | protein | 10 | 60% helix, 0% strand | B5MCN7 |
Ligands and binding sites
- M7E · 1-alpha-hydroxy-27-nor-25-O-carbonyl-vitamin D3 · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.86 | 0.95 | 41 | M7E |
| 2 | 164 | 0.46 | 0.76 | 28 | empty |
| 3 | 62 | 0.32 | 0.76 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 555 Ų buried · 6 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 B5MCN7
- Elsewhere: RCSB PDB 5E7V · PDBe 5E7V · UniProt Q9PTN2 · UniProt B5MCN7
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