Research workbench
Crystal structure of BRD9 bromodomain in complex with a substituted valerolactam quinolone ligand
Analyse Crystal structure of BRD9 bromodomain in complex with a substituted… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z6I
- Type
- protein
- Length
- 226 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 9
- UniProt
- Q9H8M2
- Ligands
- 4L3
- Pockets
- 3 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bromodomain-containing protein 9 | protein | 113 | 64% helix, 0% strand | Q9H8M2 |
Ligands and binding sites
- 4L3 · tert-butyl [(2R,3S)-1-(1,4-dimethyl-2-oxo-1,2-dihydroquinolin-7-yl)-6-oxo-2-phenylpiperidin-3-yl]carbamate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.43 | 0.82 | 14 | 4L3 |
| 2 | 72 | 0.42 | 0.80 | 17 | 4L3 |
| 3 | 63 | 0.31 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 896 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4Z6I · Crystal structure of BRD9 bromodomain in complex with a substituted valerolactam… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H8M2 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 9 (Q9H8M2) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q9H8M2
- Elsewhere: RCSB PDB 4Z6I · PDBe 4Z6I · UniProt Q9H8M2
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