Research workbench
Crystal structure of human BRD9 bromodomain in complex with LP99 chemical probe
Analyse Crystal structure of human BRD9 bromodomain in complex with LP99 chemical probe in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IGN
- 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
- 6B2
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bromodomain-containing protein 9 | protein | 113 | 63% helix, 0% strand | Q9H8M2 |
Ligands and binding sites
- 6B2 · N-[(2R,3S)-2-(4-chlorophenyl)-1-(1,4-dimethyl-2-oxo-1,2-dihydroquinolin-7-yl)-6-oxopiperidin-3-yl]-2-methylpropane-1-sulfonamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.46 | 0.82 | 18 | 6B2 |
| 2 | 69 | 0.45 | 0.82 | 18 | 6B2 |
Interfaces
1 interface between chains.
- A–B · 899 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5IGN · Crystal structure of human BRD9 bromodomain in complex with LP99 chemical probe · 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 0.92
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 5IGN · PDBe 5IGN · UniProt Q9H8M2
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