Research workbench
Crystal structure of the human vaccinia-related kinase bound to a phenyl-pteridinone inhibitor
Analyse Crystal structure of the human vaccinia-related kinase bound to a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BTW
- Type
- protein
- Length
- 1,240 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase VRK1
- EC
- 2.7.11.1
- UniProt
- Q99986
- Ligands
- E8D, CL, SO4
- Pockets
- 15 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 317 | 39% helix, 19% strand | Q99986 |
| B | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 301 | 43% helix, 17% strand | Q99986 |
| C | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 315 | 40% helix, 19% strand | Q99986 |
| D | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 307 | 40% helix, 20% strand | Q99986 |
Ligands and binding sites
- E8D · 2-[(3,5-difluoro-4-hydroxyphenyl)amino]-8-phenyl-7,8-dihydropteridin-6(5H)-one · ligand · 3 copies · chains A, B, D
- CL · Chloride ion · ion · 9 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains C
- GOL · Glycerol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.71 | 0.78 | 67 | CL |
| 2 | 765 | 0.69 | 0.76 | 78 | empty |
| 3 | 53 | 0.57 | 0.91 | 19 | empty |
| 4 | 51 | 0.57 | 0.91 | 17 | empty |
| 5 | 187 | 0.52 | 0.77 | 28 | E8D |
Interfaces
2 interfaces between chains.
- C–D · 194 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 182 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6BTW · Crystal Structure of the Human vaccinia-related kinase bound to a phenyl-pteridi inhibitor · 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 Q99986
- Elsewhere: RCSB PDB 6BTW · PDBe 6BTW · UniProt Q99986
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.