Research workbench
Crystal structure of the first bromodomain of human brdt in complex with the inhibitor JQ1
Analyse Crystal structure of the first bromodomain of human brdt in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FLP
- Type
- protein
- Length
- 213 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain testis-specific protein
- UniProt
- Q58F21
- Ligands
- JQ1, K
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain testis-specific protein | protein | 106 | 68% helix, 0% strand | Q58F21 |
| B | Bromodomain testis-specific protein | protein | 107 | 71% helix, 0% strand | Q58F21 |
Ligands and binding sites
- JQ1 · (6S)-6-(2-tert-butoxy-2-oxoethyl)-4-(4-chlorophenyl)-2,3,9-trimethyl-6,7-dihydrothieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-10-ium · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · chains 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 | 348 | 0.60 | 0.77 | 27 | empty |
| 2 | 127 | 0.52 | 0.80 | 18 | JQ1 |
| 3 | 123 | 0.51 | 0.80 | 18 | JQ1 |
Interfaces
1 interface between chains.
- A–B · 230 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4FLP · Crystal Structure of the first bromodomain of human BRDT in complex with the inhibitor JQ1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q58F21 · AlphaFold monomer V2.0 prediction for bromodomain testis-specific protein (Q58F21) · 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 Q58F21
- Elsewhere: RCSB PDB 4FLP · PDBe 4FLP · UniProt Q58F21
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