MolNFT v1 · #111807 · protein
Crystal structure of the first bromodomain of human BRD4 bound to benzotriazolo-diazepine scaffold
4Z1Q · Bromodomain-containing protein 4: “Crystal structure of the first bromodomain of human BRD4 bound to benzotriazolo-diazepine scaffold”. X-ray diffraction, 1 ligand (558), 3 pockets (best druggability 0.57). MolNFT v1 #111807 on…
- PDB
- 4Z1Q
- Type
- protein
- Length
- 251 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 4
- UniProt
- O60885
- Ligands
- 558
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 4 | protein | 124 | 53% helix, 0% strand | O60885 |
| B | Bromodomain-containing protein 4 | protein | 127 | 52% helix, 0% strand | O60885 |
Ligands and binding sites
- 558 · 5-[(4R)-6-(4-chlorophenyl)-1,4-dimethyl-5,6-dihydro-4H-[1,2,4]triazolo[4,3-a][1,5]benzodiazepin-8-yl]pyridin-2-amine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.57 | 0.75 | 34 | empty |
| 2 | 148 | 0.55 | 0.81 | 26 | 558 |
| 3 | 120 | 0.50 | 0.80 | 18 | 558 |
Interfaces
1 interface between chains.
- A–B · 476 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4Z1Q · Crystal structure of the first bromodomain of human BRD4 bound to benzotriazolo-diazepine… · 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 4Z1Q · PDBe 4Z1Q · UniProt O60885
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