MolNFT v1 · #158295 · protein
Crystal structure of the human vaccinia-related kinase bound to a N,N- dipropynyl-dihydropteridine-3-hydroxyindazole inhibitor
6NPN · SERINE/THREONINE-protein kinase VRK1: “Crystal structure of the human vaccinia-related kinase bound to a N,N…”. X-ray diffraction, 2 ligands (KWJ, SO4), 14 pockets (best druggability 0.72). MolNFT v1 #158295 on GenesisL1: 3D…
- PDB
- 6NPN
- Type
- protein
- Length
- 1,244 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
- KWJ, SO4
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 17% 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 | 301 | 43% helix, 16% strand | Q99986 |
| C | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 315 | 39% helix, 18% strand | Q99986 |
| D | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 311 | 40% helix, 17% strand | Q99986 |
Ligands and binding sites
- KWJ · (7R)-7-methyl-2-[(3-oxo-2,3-dihydro-1H-indazol-6-yl) amino]-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.72 | 0.78 | 76 | EDO |
| 2 | 606 | 0.70 | 0.78 | 63 | SO4 |
| 3 | 52 | 0.63 | 0.94 | 18 | PEG |
| 4 | 59 | 0.62 | 0.92 | 17 | empty |
| 5 | 215 | 0.57 | 0.79 | 29 | KWJ |
Interfaces
2 interfaces between chains.
- A–B · 313 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 224 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6NPN · 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 6NPN · PDBe 6NPN · UniProt Q99986
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