Research workbench
Structure-based design of a superagonist ligand for the vitamin D nuclear receptor
Analyse Structure-based design of a superagonist ligand for the vitamin D nuclear… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CS4
- Type
- protein
- Length
- 254 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor
- UniProt
- P11473
- Ligands
- COV
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 254 | 66% helix, 3% strand | P11473 |
Ligands and binding sites
- COV · (1S,3R,5Z,7E,14beta,17alpha)-17-[(2S,4S)-4-(2-hydroxy-2-methylpropyl)-2-methyltetrahydrofuran-2-yl]-9,10-secoandrosta-5,7,10-triene-1,3-diol · 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 | 312 | 0.86 | 0.95 | 36 | COV |
| 2 | 66 | 0.31 | 0.75 | 15 | empty |
Compared structures
- 3CS4 · Structure-based design of a superagonist ligand for the vitamin D nuclear receptor · the same entry in another collection · chain A against A, TM-score 1.00
- P11473 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor (P11473) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P11473
- Elsewhere: RCSB PDB 3CS4 · PDBe 3CS4 · UniProt P11473
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