MolNFT v1 · #56638 · protein
2-substituted-16-ene-22-thia-1ALPHA,25-dihydroxy-26,27- dimethyl-19-norvitamin D3 analogs: synthesis, biological evaluation and crystal structure
2ZLC · Vitamin D3 receptor: “2-substituted-16-ene-22-thia-1ALPHA,25-dihydroxy-26,27- dimethyl-19-norvitamin D3 analogs: synthesis…”. X-ray diffraction, 1 ligand (VDX), 2 pockets (best druggability 0.86). MolNFT v1 #56638 on GenesisL1: 3D…
- PDB
- 2ZLC
- Type
- protein
- Length
- 251 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor; Coactivator peptide drip
- UniProt
- P13053
- Ligands
- VDX
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 240 | 67% helix, 3% strand | P13053 |
| C | Coactivator peptide drip | protein | 11 | 64% helix, 0% strand | — |
Ligands and binding sites
- VDX · 5-{2-[1-(5-hydroxy-1,5-dimethyl-hexyl)-7A-methyl-octahydro-inden-4-ylidene]-ethylidene}-4-methylene-cyclohexane-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 | 315 | 0.86 | 0.96 | 39 | VDX |
| 2 | 90 | 0.37 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–C · 564 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2ZLC · 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs… · the same entry in another collection · chain A against A, TM-score 1.00
- P13053 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor (P13053) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P13053
- Elsewhere: RCSB PDB 2ZLC · PDBe 2ZLC · UniProt P13053
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