MolNFT v1 · #190172 · protein
Crystal structure of the first bromodomain of human BRD4 in complex with the inhibitor Y13153
7WKY · Bromodomain-containing protein 4: “Crystal structure of the first bromodomain of human BRD4 in complex with the inhibitor Y13153”. X-ray diffraction, 1 ligand (JFR), 4 pockets (best druggability 0.71). MolNFT v1 #190172 on…
- PDB
- 7WKY
- Type
- protein
- Length
- 328 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- JFR
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bromodomain-containing protein 4 | protein | 109 | 62% helix, 0% strand | O60885 |
| C | Bromodomain-containing protein 4 | protein | 110 | 65% helix, 0% strand | O60885 |
Ligands and binding sites
- JFR · 2-(2-cyclopentyl-1~{H}-imidazol-5-yl)-7-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-5-methyl-furo[3,2-c]pyridin-4-one · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.71 | 0.78 | 53 | JFR, GOL |
| 2 | 105 | 0.48 | 0.80 | 20 | JFR |
| 3 | 104 | 0.42 | 0.77 | 22 | empty |
| 4 | 86 | 0.38 | 0.76 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–C · 378 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 338 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7WKY · Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor… · 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 0.99
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 7WKY · PDBe 7WKY · UniProt O60885
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