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Crystal structure of the first bromodomain (BD1) of human BRD4 (BRD4- 1) in complex with bivalent inhibitor nc-III-49-1
Analyse Crystal structure of the first bromodomain (BD1) of human BRD4 (BRD4- 1) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LA9
- Type
- protein
- Length
- 630 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- XR7, NA, CL
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Bromodomain-containing protein 4 | protein | 105 | 67% helix, 0% strand | O60885 |
Ligands and binding sites
- XR7 · N,N'-(oxybis{(ethane-2,1-diyl)oxyethane-2,1-diyloxy[3-(2-methyl-1-oxo-1,2-dihydroisoquinolin-4-yl)-4,1-phenylene]})di(ethane-1-sulfonamide) · ligand · 3 copies · chains A, D, B, F, C, E
- NA · Sodium ion · metal · chains C
- CL · Chloride ion · ion · 8 copies · chains A, B, F, C, D, E
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, D, C, E, F
- PEG · Di(hydroxyethyl)ether · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.70 | 0.79 | 47 | XR7, EDO |
| 2 | 522 | 0.69 | 0.78 | 44 | XR7 |
| 3 | 521 | 0.67 | 0.77 | 47 | XR7, EDO |
| 4 | 308 | 0.55 | 0.75 | 37 | EDO |
| 5 | 119 | 0.43 | 0.76 | 14 | CL |
Interfaces
6 interfaces between chains.
- A–B · 744 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 394 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 384 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 359 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 343 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7LA9 · Crystal structure of the first bromodomain (BD1) of human BRD4 (BRD4-1) in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
- O60885 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 4 (O60885) · a predicted model of the same protein · chain F 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 7LA9 · PDBe 7LA9 · UniProt O60885
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