Research workbench
Crystal structure of the second bromodomain of human BRD4 with the inhibitor GW841819X
Analyse Crystal structure of the second bromodomain of human BRD4 with the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YEM
- Type
- protein
- Length
- 221 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- WSH
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 110 | 71% helix, 0% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 111 | 70% helix, 0% strand | O60885 |
Ligands and binding sites
- WSH · Benzyl [(4R)-1-methyl-6-phenyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]carbamate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.52 | 0.78 | 20 | empty |
| 2 | 104 | 0.51 | 0.81 | 20 | WSH |
| 3 | 119 | 0.50 | 0.80 | 21 | WSH |
| 4 | 153 | 0.48 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 782 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2YEM · Crystal Structure of the Second Bromodomain of Human Brd4 with the inhibitor GW841819X · 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 2YEM · PDBe 2YEM · UniProt O60885
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