Research workbench
Crystal structure of BRD9 bromodomain in complex with an indolizine ligand
Analyse Crystal structure of BRD9 bromodomain in complex with an indolizine ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E9V
- 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
- 5L0
- Pockets
- 3 · best druggability 0.64
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
- 5L0 · 1-[1-(imidazo[1,2-a]pyridin-5-yl)-7-(morpholin-4-yl)indolizin-3-yl]ethanone · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.64 | 0.75 | 48 | empty |
| 2 | 109 | 0.51 | 0.81 | 18 | 5L0 |
| 3 | 84 | 0.50 | 0.83 | 18 | 5L0 |
Interfaces
1 interface between chains.
- A–B · 253 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5E9V · Crystal structure of BRD9 bromodomain in complex with an indolizine ligand · 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 A 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 5E9V · PDBe 5E9V · UniProt Q9H8M2
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