Research workbench
BRD4_BROMODOMAIN2 complex with pyrrolopyridone compound 18
Analyse BRD4_BROMODOMAIN2 complex with pyrrolopyridone compound 18 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VIX
- Type
- protein
- Length
- 430 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- QYV
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Bromodomain-containing protein 4 | protein | 107 | 69% helix, 0% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 108 | 72% helix, 0% strand | O60885 |
| C | Bromodomain-containing protein 4 | protein | 108 | 71% helix, 0% strand | O60885 |
Ligands and binding sites
- QYV · 4-[2-(2,4-difluorophenoxy)-5-(methylsulfonyl)phenyl]-N-ethyl-6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-2-carboxamide · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.77 | 0.81 | 60 | QYV |
| 2 | 314 | 0.55 | 0.75 | 42 | empty |
| 3 | 317 | 0.55 | 0.75 | 37 | empty |
| 4 | 120 | 0.51 | 0.80 | 21 | QYV |
| 5 | 108 | 0.48 | 0.80 | 20 | QYV |
Interfaces
3 interfaces between chains.
- B–C · 739 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 716 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 358 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VIX · BRD4_Bromodomain2 complex with pyrrolopyridone compound 18 · the same entry in another collection · chain D against D, TM-score 1.00
- O60885 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 4 (O60885) · a predicted model of the same protein · chain D 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 6VIX · PDBe 6VIX · UniProt O60885
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.