Research workbench
Crystal structure of the bromodomain of BRD9 in complex with compound 9.
Analyse Crystal structure of the bromodomain of BRD9 in complex with compound 9. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F1L
- Type
- protein
- Length
- 227 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 9
- UniProt
- Q9H8M2
- Ligands
- 5U2
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 9 | protein | 113 | 63% helix, 0% strand | Q9H8M2 |
| B | Bromodomain-containing protein 9 | protein | 114 | 62% helix, 0% strand | Q9H8M2 |
Ligands and binding sites
- 5U2 · 5-[3,5-dimethoxy-4-[(3-oxidanylazetidin-1-yl)methyl]phenyl]-1,3-dimethyl-pyridin-2-one · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.55 | 0.83 | 20 | 5U2 |
| 2 | 80 | 0.46 | 0.81 | 18 | 5U2 |
| 3 | 65 | 0.32 | 0.75 | 16 | empty |
| 4 | 56 | 0.29 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 926 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5F1L · Crystal structure of the bromodomain of BRD9 in complex with compound 9. · 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 5F1L · PDBe 5F1L · UniProt Q9H8M2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.