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Crystal structure of the first bromodomain (BD1) of human BRD4 bound to ERK5-IN-1
Analyse Crystal structure of the first bromodomain (BD1) of human BRD4 bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K6G
- Type
- protein
- Length
- 254 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Homo sapiens
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- VYJ
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · resolution 1.7 · 1 distinct chain · 53% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bromodomain-containing protein 4 | protein | 127 | 53% helix, 0% strand | O60885 |
Ligands and binding sites
- VYJ · 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one · ligand · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.66 | 0.76 | 57 | EDO |
| 2 | 136 | 0.55 | 0.81 | 25 | VYJ |
| 3 | 120 | 0.54 | 0.82 | 20 | VYJ |
Interfaces
1 interface between chains.
- A–B · 327 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7K6G · Crystal structure of the first bromodomain (BD1) of human BRD4 bound to ERK5-in-1 · the same entry in another collection · chain A against A, TM-score 1.00
- O60885 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 4 (O60885) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O60885
- Elsewhere: RCSB PDB 7K6G · PDBe 7K6G · UniProt O60885
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