MolNFT v1 · #169289 · protein
BRD4 bromodomain 1 in complex with multi-action inhibitor SRX3212P
6X7B · Bromodomain-containing protein 4: “BRD4 bromodomain 1 in complex with multi-action inhibitor SRX3212P”. X-ray diffraction, 1 ligand (ZVP), 4 pockets (best druggability 0.51). MolNFT v1 #169289 on GenesisL1: 3D structure, binding…
- PDB
- 6X7B
- Type
- protein
- Length
- 265 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- ZVP
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 134 | 49% helix, 7% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 131 | 52% helix, 3% strand | O60885 |
Ligands and binding sites
- ZVP · 7-[7-oxo-5-(piperazin-1-yl)-7H-thieno[3,2-b]pyran-3-yl]-N-[(pyridin-3-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxamide · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.51 | 0.82 | 19 | ZVP |
| 2 | 85 | 0.49 | 0.82 | 17 | ZVP |
| 3 | 64 | 0.47 | 0.84 | 19 | empty |
| 4 | 66 | 0.37 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 720 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6X7B · BRD4 Bromodomain 1 in complex with multi-action inhibitor SRX3212P · 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 6X7B · PDBe 6X7B · UniProt O60885
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