MolNFT v1 · #118429 · protein
Crystal structure of the bromodomain of BRD9 in complex with compound 9.
5F1L · Bromodomain-containing protein 9: “Crystal structure of the bromodomain of BRD9 in complex with compound 9.”. X-ray diffraction, 1 ligand (5U2), 4 pockets (best druggability 0.55). MolNFT v1 #118429 on GenesisL1: 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
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