Research workbench
BRD4 bromodomain 1 in complex with multi-action inhibitor SF2523P
Analyse BRD4 bromodomain 1 in complex with multi-action inhibitor SF2523P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X7D
- Type
- protein
- Length
- 252 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- UT4
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 124 | 58% helix, 0% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 128 | 52% helix, 2% strand | O60885 |
Ligands and binding sites
- UT4 · 3-(2,3-dihydro-1,4-benzodioxin-6-yl)-5-(piperazin-1-yl)-7H-thieno[3,2-b]pyran-7-one · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.56 | 0.82 | 24 | UT4 |
| 2 | 109 | 0.55 | 0.83 | 17 | UT4 |
| 3 | 68 | 0.41 | 0.80 | 12 | empty |
| 4 | 59 | 0.33 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 670 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6X7D · BRD4 Bromodomain 1 in complex with multi-action inhibitor SF2523P · 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 6X7D · PDBe 6X7D · UniProt O60885
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