Research workbench
Crystal structure of the first bromodomain of human BRD4 in complex with 2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9- [(S)-(oxan-4-YL)(PHENYL)METHYL]-9H-carbazole-4-carboxamide
Analyse Crystal structure of the first bromodomain of human BRD4 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5S9Q
- Type
- protein
- Length
- 510 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- YW7
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Bromodomain-containing protein 4 | protein | 127 | 53% helix, 0% strand | O60885 |
| B, D | Bromodomain-containing protein 4 | protein | 128 | 55% helix, 0% strand | O60885 |
Ligands and binding sites
- YW7 · 2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9-[(S)-(oxan-4-yl)(phenyl)methyl]-9H-carbazole-4-carboxamide · ligand · 4 copies · chains A, B, D, E
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.74 | 0.80 | 68 | EDO |
| 2 | 330 | 0.60 | 0.78 | 39 | empty |
| 3 | 318 | 0.58 | 0.77 | 33 | empty |
| 4 | 141 | 0.57 | 0.82 | 27 | YW7 |
| 5 | 130 | 0.55 | 0.82 | 19 | YW7 |
Interfaces
5 interfaces between chains.
- B–E · 588 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 421 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 287 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 254 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5S9Q · CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH… · the same entry in another collection · chain E against E, 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 5S9Q · PDBe 5S9Q · UniProt O60885
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