MolNFT v1 · #113777 · protein
Ligand complex of rorg lbd
5APH · Nuclear receptor ror-gamma: “Ligand complex of rorg lbd”. X-ray diffraction, 1 ligand (VYI), 4 pockets (best druggability 0.82). MolNFT v1 #113777 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5APH
- Type
- protein
- Length
- 264 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma; Nuclear receptor coactivator 2
- UniProt
- P51449, E7EWM1
- Ligands
- VYI
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor ror-gamma | protein | 252 | 73% helix, 4% strand | P51449 |
| C | Nuclear receptor coactivator 2 | protein | 12 | 50% helix, 0% strand | E7EWM1 |
Ligands and binding sites
- VYI · N-(2-fluorophenyl)-4-[(4-fluorophenyl)sulfonyl]-2,3,4,5-tetrahydro-1,4-benzoxazepin-6-amine · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.82 | 0.90 | 32 | VYI, DMS |
| 2 | 96 | 0.43 | 0.79 | 18 | empty |
| 3 | 80 | 0.41 | 0.79 | 17 | empty |
| 4 | 90 | 0.34 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 573 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5APH · Ligand complex of RORg LBD · 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
- Every structure of UniProt E7EWM1
- Elsewhere: RCSB PDB 5APH · PDBe 5APH · UniProt P51449 · UniProt E7EWM1
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