Research workbench
Ror gamma in complex with SCR2 and compound 3
Analyse Ror gamma in complex with SCR2 and compound 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KCO
- Type
- protein
- Length
- 520 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma; Peptide glu-lys-his-lys-ile-leu-his-arg-leu-leu-gln-asp- ser
- UniProt
- P51449
- Ligands
- WB7
- Pockets
- 8 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nuclear receptor ror-gamma | protein | 248 | 71% helix, 4% strand | P51449 |
| C | Peptide glu-lys-his-lys-ile-leu-his-arg-leu-leu-gln-asp- ser | protein | 11 | 73% helix, 0% strand | — |
| D | Peptide glu-lys-his-lys-ile-leu-his-arg-leu-leu-gln-asp- ser | protein | 13 | 62% helix, 0% strand | — |
Ligands and binding sites
- WB7 · 1-[(2-chlorophenyl)methyl]-N-{[4-(methylsulfonyl) phenyl]methyl}-4',5'-dihydrospiro[piperidine-4,7'-thieno[2,3-c]pyran]-2'-carboxamide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.90 | 0.91 | 112 | WB7 |
| 2 | 200 | 0.53 | 0.78 | 30 | empty |
| 3 | 105 | 0.49 | 0.81 | 17 | empty |
| 4 | 192 | 0.48 | 0.76 | 23 | empty |
| 5 | 62 | 0.40 | 0.80 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1110 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 582 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 519 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 204 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 179 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7KCO · ROR gamma in complex with SCR2 and compound 3 · 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 7KCO · PDBe 7KCO · UniProt P51449
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