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Crystal structure of human bromodomain-containing protein 4 (BRD4) bromodomain with MS645
Analyse Crystal structure of human bromodomain-containing protein 4 (BRD4) bromodomain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DJC
- Type
- protein
- Length
- 262 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- CF6
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 131 | 50% helix, 2% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 131 | 50% helix, 3% strand | O60885 |
Ligands and binding sites
- CF6 · N,N'-(decane-1,10-diyl)bis{2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetamide} · ligand · chains A
- EDO · 1,2-ethanediol · additive · 8 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 | 171 | 0.57 | 0.81 | 24 | empty |
| 2 | 132 | 0.52 | 0.80 | 22 | empty |
| 3 | 106 | 0.51 | 0.81 | 19 | empty |
| 4 | 68 | 0.30 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 372 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6DJC · Crystal structure of human Bromodomain-containing protein 4 (BRD4) bromodomain with MS645 · 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 6DJC · PDBe 6DJC · UniProt O60885
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