Research workbench
Bromodomain of trypanosoma brucei BDF2 with ibet-151
Analyse Bromodomain of trypanosoma brucei BDF2 with ibet-151 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PKL
- Type
- protein
- Length
- 218 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain factor 2
- UniProt
- Q38AM1
- Ligands
- 1GH, K, PO4, CL
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain factor 2 | protein | 110 | 60% helix, 0% strand | Q38AM1 |
| B | Bromodomain factor 2 | protein | 108 | 60% helix, 0% strand | Q38AM1 |
Ligands and binding sites
- 1GH · 7-(3,5-dimethyl-1,2-oxazol-4-yl)-8-methoxy-1-[(1R)-1-(pyridin-2-yl)ethyl]-1H,2H,3H-imidazo[4,5-c]quinolin-2-one · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.75 | 0.85 | 38 | 1GH |
| 2 | 114 | 0.48 | 0.80 | 23 | 1GH |
Interfaces
1 interface between chains.
- A–B · 428 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4PKL · Bromodomain of Trypanosoma brucei BDF2 With IBET-151 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q38AM1
- Elsewhere: RCSB PDB 4PKL · PDBe 4PKL · UniProt Q38AM1
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