Research workbench
Rorgamma in complex with inverse agonist 4J.
Analyse Rorgamma in complex with inverse agonist 4J. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZOM
- Type
- protein
- Length
- 879 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma
- UniProt
- P51449
- Ligands
- 4Q3
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor ror-gamma | protein | 223 | 71% helix, 4% strand | P51449 |
| B | Nuclear receptor ror-gamma | protein | 222 | 72% helix, 5% strand | P51449 |
| C | Nuclear receptor ror-gamma | protein | 219 | 70% helix, 5% strand | P51449 |
| D | Nuclear receptor ror-gamma | protein | 215 | 72% helix, 5% strand | P51449 |
Ligands and binding sites
- 4Q3 · N-{4-[3-(acetylamino)-1-(propan-2-yl)-1H-pyrazol-5-yl]-2-[(1R,5S)-3-azabicyclo[3.1.0]hex-3-yl]phenyl}-2-chloro-6-fluoro-N-methylbenzamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.83 | 0.90 | 35 | 4Q3 |
| 2 | 425 | 0.82 | 0.90 | 36 | 4Q3 |
| 3 | 502 | 0.80 | 0.86 | 41 | 4Q3 |
| 4 | 529 | 0.79 | 0.85 | 48 | 4Q3 |
| 5 | 196 | 0.52 | 0.78 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–C · 893 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 798 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 87 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 65 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ZOM · RORgamma in complex with inverse agonist 4j. · 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 4ZOM · PDBe 4ZOM · UniProt P51449
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