Research workbench
Crystal structure of the bromodomain (bd) of human bromodomain and phd finger-containing transcription factor (bptf) bound to compound 6 (HZ01052)
Analyse Crystal structure of the bromodomain (bd) of human bromodomain and phd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KDW
- Type
- protein
- Length
- 227 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleosome-remodeling factor subunit bptf
- UniProt
- Q12830
- Ligands
- WCV
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleosome-remodeling factor subunit bptf | protein | 113 | 66% helix, 2% strand | Q12830 |
| B | Nucleosome-remodeling factor subunit bptf | protein | 114 | 69% helix, 2% strand | Q12830 |
Ligands and binding sites
- WCV · cyclopropyl[7-({2-[(prop-2-yn-1-yl)amino]pyrimidin-4-yl}amino)-3,4-dihydroquinolin-1(2H)-yl]methanone · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 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 | 112 | 0.54 | 0.83 | 20 | WCV |
| 2 | 264 | 0.54 | 0.76 | 33 | EDO |
| 3 | 114 | 0.53 | 0.82 | 19 | WCV |
Interfaces
1 interface between chains.
- A–B · 276 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7KDW · Crystal structure of the bromodomain (BD) of human Bromodomain and PHD finger-containing… · 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 7KDW · PDBe 7KDW · UniProt Q12830
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.