Research workbench
N-terminal bromodomain of human BRD4 with 1-(2R,4S)-2- methyl-4-(phenylamino)-6-4-(piperidin-1-YLMETHYL)PHENYL- 1,2,3,4-tetrahydroquinolin-1-yl-ethan-1-one
Analyse N-terminal bromodomain of human BRD4 with 1-(2R,4S)-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ACY
- Type
- protein
- Length
- 254 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- 9S3
- Pockets
- 4 · best druggability 0.63
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 | 127 | 53% helix, 0% strand | O60885 |
Ligands and binding sites
- 9S3 · 1-[(2S,4R)-2-methyl-4-(phenylamino)-6-[4-(piperidin-1-ylmethyl)phenyl]-3,4-dihydroquinolin-1(2H)-yl]ethanone · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 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 | 361 | 0.63 | 0.79 | 40 | empty |
| 2 | 101 | 0.52 | 0.82 | 19 | 9S3 |
| 3 | 115 | 0.50 | 0.80 | 19 | 9S3 |
| 4 | 92 | 0.34 | 0.74 | 21 | EDO |
Interfaces
1 interface between chains.
- A–B · 365 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ACY · N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1-(2R,4S)-2-methyl-4-(phenylamino)-6-4-(piperidi… · 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 5ACY · PDBe 5ACY · UniProt O60885
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