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Crystal structure of the human vaccinia-related kinase bound to a N- methyl-N-propyl-dihydropteridine inhibitor
Analyse Crystal structure of the human vaccinia-related kinase bound to a N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CSW
- Type
- protein
- Length
- 1,255 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
- FBY, SO4, CL
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 316 | 41% helix, 19% strand | Q99986 |
| B | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 308 | 42% helix, 16% strand | Q99986 |
| C | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 319 | 40% helix, 19% strand | Q99986 |
| D | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 312 | 40% helix, 18% strand | Q99986 |
Ligands and binding sites
- FBY · (7R)-5-butyl-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7, 8-dimethyl-7,8-dihydropteridin-6(5H)-one · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains C, D
- GOL · Glycerol · additive · 15 copies · chains B, A, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.74 | 0.78 | 82 | PG4, SO4, GOL |
| 2 | 743 | 0.72 | 0.78 | 78 | GOL, SO4 |
| 3 | 244 | 0.61 | 0.80 | 29 | FBY, GOL |
| 4 | 58 | 0.59 | 0.91 | 18 | empty |
| 5 | 150 | 0.51 | 0.80 | 35 | empty |
Interfaces
2 interfaces between chains.
- C–D · 287 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 285 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6CSW · Crystal Structure of the Human vaccinia-related kinase bound to a… · 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 6CSW · PDBe 6CSW · UniProt Q99986
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