MolNFT v1 · #136767 · protein
Crystal structure of human vitamin D receptor ligand binding domain in complex with a vdrm
5V39 · Vitamin D3 receptor: “Crystal structure of human vitamin D receptor ligand binding domain in complex with a vdrm”. X-ray diffraction, 1 ligand (8VM), 2 pockets (best druggability 0.86). MolNFT v1 #136767 on GenesisL1: 3D structure…
- PDB
- 5V39
- Type
- protein
- Length
- 251 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor
- UniProt
- P11473
- Ligands
- 8VM
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 251 | 65% helix, 3% strand | P11473 |
Ligands and binding sites
- 8VM · 5-(3-{4-[(2S)-2-hydroxy-3,3-dimethylbutoxy]-3-methylphenyl}pentan-3-yl)-3-methyl-N-(1H-tetrazol-5-yl)thiophene-2-carboxamide · 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 | 297 | 0.86 | 0.96 | 35 | 8VM |
| 2 | 56 | 0.33 | 0.77 | 9 | empty |
Compared structures
- 5V39 · Crystal structure of human vitamin D receptor ligand binding domain in complex with a VDRM · the same entry in another collection · chain A against A, TM-score 1.00
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 5V39 · PDBe 5V39 · UniProt P11473
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