Research workbench
Side-chain fluorine atoms of non-steroidal vitamin D3 analogs stabilize helix 12 of vitamin D receptor
Analyse Side-chain fluorine atoms of non-steroidal vitamin D3 analogs stabilize helix… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DR1
- Type
- protein
- Length
- 251 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor a; Src-1 (lxxll motif) from nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- Q9PTN2, Q15788
- Ligands
- C5D, MG
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor a | protein | 240 | 67% helix, 3% strand | Q9PTN2 |
| B | Src-1 (lxxll motif) from nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 11 | 55% helix, 0% strand | Q15788 |
Ligands and binding sites
- C5D · (1R,3R)-5-[(2E)-3-{(1S,3R)-2,2,3-trimethyl-3-[6,6,6-trifluoro-5-hydroxy-5-(trifluoromethyl)hex-3-yn-1-yl]cyclopentyl}prop-2-en-1-ylidene]cyclohexane-1,3-diol · ligand · chains A
- MG · Magnesium ion · metal · 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 | 316 | 0.86 | 0.96 | 38 | C5D |
| 2 | 182 | 0.46 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 609 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3DR1 · Side-chain fluorine atoms of non-steroidal vitamin D3 analogs stabilize helix 12 of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9PTN2 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor a (Q9PTN2) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 3DR1 · PDBe 3DR1 · UniProt Q9PTN2 · UniProt Q15788
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