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Crystal structure of the first bromodomain of human BRD4 in complex with midazolam
Analyse Crystal structure of the first bromodomain of human BRD4 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U5K
- Type
- protein
- Length
- 496 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- 08J
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 126 | 54% helix, 0% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 124 | 53% helix, 0% strand | O60885 |
| C | Bromodomain-containing protein 4 | protein | 123 | 53% helix, 0% strand | O60885 |
| D | Bromodomain-containing protein 4 | protein | 123 | 54% helix, 0% strand | O60885 |
Ligands and binding sites
- 08J · 8-chloro-6-(2-fluorophenyl)-1-methyl-4H-imidazo[1,5-a][1,4]benzodiazepine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.66 | 0.76 | 50 | empty |
| 2 | 384 | 0.63 | 0.78 | 41 | empty |
| 3 | 114 | 0.54 | 0.82 | 18 | 08J |
| 4 | 93 | 0.53 | 0.83 | 18 | 08J |
| 5 | 157 | 0.53 | 0.79 | 20 | 08J |
Interfaces
5 interfaces between chains.
- B–D · 387 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 387 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 345 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 162 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 57 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3U5K · Crystal Structure of the first bromodomain of human BRD4 in complex with Midazolam · the same entry in another collection · chain D against D, TM-score 1.00
- O60885 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 4 (O60885) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 3U5K · PDBe 3U5K · UniProt O60885
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