MolNFT v1 · #139220 · protein
Crystal structure of the mutant human ror gamma ligand binding domain with compound a.
5X8X · Nuclear receptor ror-gamma: “Crystal structure of the mutant human ror gamma ligand binding domain with compound a.”. X-ray diffraction, 1 ligand (82O), 17 pockets (best druggability 0.84). MolNFT v1 #139220 on GenesisL1: 3D…
- PDB
- 5X8X
- Type
- protein
- Length
- 965 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma; Nuclear receptor corepressor 2
- UniProt
- P51449, Q9Y618
- Ligands
- 82O
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 72% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Nuclear receptor ror-gamma | protein | 228 | 71% helix, 4% strand | P51449 |
| B | Nuclear receptor corepressor 2 | protein | 13 | 85% helix, 0% strand | Q9Y618 |
| D, H | Nuclear receptor corepressor 2 | protein | 15 | 80% helix, 0% strand | Q9Y618 |
| F | Nuclear receptor corepressor 2 | protein | 14 | 79% helix, 0% strand | Q9Y618 |
| G | Nuclear receptor ror-gamma | protein | 224 | 72% helix, 4% strand | P51449 |
Ligands and binding sites
- 82O · (3R,4R)-4-[4-cyclopropyl-5-[3-(2-methylpropyl) cyclobutyl]-1,2,4-triazol-3-yl]-N-(2,4-dimethylphenyl)-1-ethanoyl-pyrrolidine-3-carboxamide · ligand · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.84 | 0.90 | 35 | 82O |
| 2 | 459 | 0.83 | 0.90 | 35 | 82O |
| 3 | 471 | 0.83 | 0.89 | 34 | 82O |
| 4 | 387 | 0.82 | 0.90 | 35 | 82O |
| 5 | 829 | 0.78 | 0.81 | 78 | empty |
Interfaces
11 interfaces between chains.
- C–D · 776 Ų buried · 7 hydrogen bonds · protein-protein
- C–G · 775 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 759 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 758 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 703 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5X8X · Crystal Structure of the mutant Human ROR gamma Ligand Binding Domain With Compound A. · the same entry in another collection · chain H against H, TM-score 1.00
- Q9Y618 · AlphaFold monomer V2.0 prediction for nuclear receptor corepressor 2 (Q9Y618) · a predicted model of the same protein · chain B against A, TM-score 0.72
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
- Every structure of UniProt Q9Y618
- Elsewhere: RCSB PDB 5X8X · PDBe 5X8X · UniProt P51449 · UniProt Q9Y618
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