MolNFT v1 · #137973 · protein
Structure of rorgt bound to a tertiary alcohol
5W4V · Nuclear receptor ror-gamma: “Structure of rorgt bound to a tertiary alcohol”. X-ray diffraction, 1 ligand (9WA), 19 pockets (best druggability 0.82). MolNFT v1 #137973 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5W4V
- Type
- protein
- Length
- 1,235 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma
- UniProt
- P51449
- Ligands
- 9WA
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nuclear receptor ror-gamma | protein | 209 | 66% helix, 5% strand | P51449 |
| C | Nuclear receptor ror-gamma | protein | 206 | 68% helix, 5% strand | P51449 |
| D | Nuclear receptor ror-gamma | protein | 203 | 67% helix, 5% strand | P51449 |
| E | Nuclear receptor ror-gamma | protein | 206 | 66% helix, 5% strand | P51449 |
| F | Nuclear receptor ror-gamma | protein | 202 | 68% helix, 5% strand | P51449 |
Ligands and binding sites
- 9WA · (R)-(4-chloro-2-methoxy-3-{[4-(1H-pyrazol-1-yl) phenyl]methyl}quinolin-6-yl)(1-methyl-1H-imidazol-5-yl)[6-(trifluoromethyl)pyridin-3-yl]methanol · ligand · 6 copies · chains A, B, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.82 | 0.88 | 49 | 9WA |
| 2 | 462 | 0.81 | 0.88 | 51 | 9WA |
| 3 | 578 | 0.81 | 0.86 | 49 | 9WA |
| 4 | 608 | 0.80 | 0.85 | 63 | 9WA |
| 5 | 812 | 0.78 | 0.81 | 71 | 9WA |
Interfaces
6 interfaces between chains.
- A–B · 1045 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 896 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 772 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 695 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 28 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5W4V · Structure of RORgt bound to a tertiary alcohol · 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 P51449
- Elsewhere: RCSB PDB 5W4V · PDBe 5W4V · UniProt P51449
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