Research workbench
Benzopiperazine bet bromodomain inhibitor in complex with BD1 of BRD4
Analyse Benzopiperazine bet bromodomain inhibitor in complex with BD1 of BRD4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VOM
- Type
- protein
- Length
- 252 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- 9GY
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bromodomain-containing protein 4 | protein | 126 | 53% helix, 0% strand | O60885 |
Ligands and binding sites
- 9GY · 3-[(2S)-1-acetyl-4-(furan-2-carbonyl)-2-methyl-1,2,3,4-tetrahydroquinoxalin-6-yl]-N-methylbenzamide · ligand · 2 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 | 318 | 0.62 | 0.79 | 42 | empty |
| 2 | 121 | 0.54 | 0.82 | 21 | 9GY |
| 3 | 116 | 0.51 | 0.81 | 25 | 9GY |
Interfaces
1 interface between chains.
- A–B · 556 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5VOM · Benzopiperazine BET bromodomain inhibitor in complex with BD1 of Brd4 · 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 5VOM · PDBe 5VOM · UniProt O60885
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