Research workbench
Crystal structure of the BRD9 bromodomain in complex with compound 4.
Analyse Crystal structure of the BRD9 bromodomain in complex with compound 4. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F25
- Type
- protein
- Length
- 226 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BRD9
- UniProt
- Q9H8M2
- Ligands
- 5TU
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BRD9 | protein | 113 | 63% helix, 0% strand | Q9H8M2 |
| B | BRD9 | protein | 113 | 64% helix, 0% strand | Q9H8M2 |
Ligands and binding sites
- 5TU · 4-(1,5-dimethyl-6-oxidanylidene-pyridin-3-yl)benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.50 | 0.83 | 15 | 5TU |
| 2 | 76 | 0.48 | 0.82 | 18 | 5TU |
| 3 | 58 | 0.30 | 0.75 | 14 | empty |
| 4 | 57 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 882 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5F25 · Crystal structure of the BRD9 bromodomain in complex with compound 4. · 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 5F25 · PDBe 5F25 · UniProt Q9H8M2
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