Research workbench
Crystal structure of bptf bromodomain in complex with inhibitor pdy-3- 093
Analyse Crystal structure of bptf bromodomain in complex with inhibitor pdy-3- 093 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LRK
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleosome-remodeling factor subunit bptf
- UniProt
- Q12830
- Ligands
- YC4
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleosome-remodeling factor subunit bptf | protein | 119 | 70% helix, 2% strand | Q12830 |
| B | Nucleosome-remodeling factor subunit bptf | protein | 123 | 74% helix, 0% strand | Q12830 |
Ligands and binding sites
- YC4 · 4-chloranyl-2-methyl-5-[[(3~{S})-pyrrolidin-3-yl]amino]pyridazin-3-one · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.58 | 0.82 | 32 | YC4 |
| 2 | 84 | 0.50 | 0.83 | 17 | YC4 |
Interfaces
1 interface between chains.
- A–B · 195 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7LRK · Crystal structure of BPTF bromodomain in complex with inhibitor Pdy-3-093 · 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 Q12830
- Elsewhere: RCSB PDB 7LRK · PDBe 7LRK · UniProt Q12830
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