MolNFT v1 · #145431 · protein
Crystal structure of the human vaccinia-related kinase 1 (VRK1) bound to an N-propynyl-N-isopentyl-dihydropteridin inhibitor
6CNX · SERINE/THREONINE-protein kinase VRK1: “Crystal structure of the human vaccinia-related kinase 1 (VRK1) bound to an…”. X-ray diffraction, 3 ligands (F87, FCS, SO4), 17 pockets (best druggability 0.70). MolNFT v1 #145431 on GenesisL1…
- PDB
- 6CNX
- Type
- protein
- Length
- 1,256 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
- F87, FCS, SO4
- Pockets
- 17 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 322 | 39% helix, 19% strand | Q99986 |
| B | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 311 | 41% helix, 19% strand | Q99986 |
| C | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 311 | 41% helix, 19% strand | Q99986 |
| D | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 312 | 42% helix, 19% strand | Q99986 |
Ligands and binding sites
- F87 · (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-8-(3-methylbutyl)-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one · ligand · 3 copies · chains A, B, D
- FCS · (7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-8-(3-methylbutyl)-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one · ligand · chains C
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, D
- ACT · Acetate ion · additive · 14 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.70 | 0.76 | 81 | empty |
| 2 | 669 | 0.69 | 0.77 | 65 | empty |
| 3 | 322 | 0.62 | 0.79 | 33 | F87 |
| 4 | 55 | 0.58 | 0.91 | 20 | empty |
| 5 | 56 | 0.58 | 0.90 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 195 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 178 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6CNX · Crystal Structure of the Human vaccinia-related kinase 1 (VRK1) bound to an… · 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 6CNX · PDBe 6CNX · UniProt Q99986
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