Research workbench
Crystal structure of the BRD7 bromodomain in complex with bi-9564
Analyse Crystal structure of the BRD7 bromodomain in complex with bi-9564 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MQ1
- Type
- protein
- Length
- 108 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 7
- UniProt
- Q9NPI1
- Ligands
- 5U6, ZN, MG, CL
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 7 | protein | 108 | 58% helix, 0% strand | Q9NPI1 |
Ligands and binding sites
- 5U6 · 4-[4-[(dimethylamino)methyl]-2,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal
- CL · Chloride ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 11 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.52 | 0.81 | 24 | 5U6 |
Compared structures
- 5MQ1 · Crystal structure of the BRD7 bromodomain in complex with BI-9564 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NPI1 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 7 (Q9NPI1) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9NPI1
- Elsewhere: RCSB PDB 5MQ1 · PDBe 5MQ1 · UniProt Q9NPI1
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