MolNFT v1 · #144288 · protein
Crystal structure of the human vaccinia-related kinase 1 bound to (R)- 2-phenylaminopteridinone inhibitor
6BP0 · SERINE/THREONINE-protein kinase VRK1: “Crystal structure of the human vaccinia-related kinase 1 bound to (R)- 2-phenylaminopteridinone inhibitor”. X-ray diffraction, 3 ligands (E1D, CL, SO4), 14 pockets (best druggability 0.71).…
- PDB
- 6BP0
- Type
- protein
- Length
- 1,247 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
- E1D, CL, SO4
- Pockets
- 14 · best druggability 0.71
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 | 317 | 39% helix, 18% strand | Q99986 |
| B | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 304 | 42% helix, 18% 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 | 311 | 41% helix, 19% strand | Q99986 |
Ligands and binding sites
- E1D · (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7,8-trimethyl-7,8-dihydropteridin-6(5H)-one · ligand · 2 copies · chains B, D
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains C, D
- EDO · 1,2-ethanediol · additive · chains B
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.71 | 0.77 | 81 | empty |
| 2 | 670 | 0.68 | 0.76 | 62 | SO4 |
| 3 | 57 | 0.58 | 0.90 | 18 | empty |
| 4 | 152 | 0.53 | 0.80 | 28 | E1D |
| 5 | 161 | 0.51 | 0.78 | 23 | empty |
Interfaces
2 interfaces between chains.
- C–D · 206 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 202 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6BP0 · Crystal Structure of the Human vaccinia-related kinase 1 bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- Q99986 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase VRK1 (Q99986) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 6BP0 · PDBe 6BP0 · UniProt Q99986
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.