Research workbench
Crystal structure of the first bromodomain of human BRD4 in complex with bi 2536
Analyse Crystal structure of the first bromodomain of human BRD4 in complex with bi 2536 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O74
- Type
- protein
- Length
- 254 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- R78
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bromodomain-containing protein 4 | protein | 127 | 54% helix, 0% strand | O60885 |
Ligands and binding sites
- R78 · 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains 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 | 613 | 0.67 | 0.76 | 58 | EDO |
| 2 | 139 | 0.53 | 0.81 | 27 | R78 |
| 3 | 116 | 0.53 | 0.82 | 19 | R78 |
Interfaces
1 interface between chains.
- A–B · 270 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4O74 · Crystal structure of the first bromodomain of human BRD4 in complex with BI 2536 · 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 B 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 4O74 · PDBe 4O74 · UniProt O60885
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