MolNFT v1 · #157844 · protein
Crystal structure of human vaccinia-related kinase 2 (vrk-2) bound to pyridin-benzenesulfonamide inhibitor
6NCG · SERINE/THREONINE-protein kinase VRK2: “Crystal structure of human vaccinia-related kinase 2 (vrk-2) bound to pyridin-benzenesulfonamide inhibitor”. X-ray diffraction, 2 ligands (KJD, SO4), 7 pockets (best druggability 0.66). MolNFT…
- PDB
- 6NCG
- Type
- protein
- Length
- 595 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase VRK2
- EC
- 2.7.11.1
- UniProt
- Q86Y07
- Ligands
- KJD, SO4
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase VRK2 (EC 2.7.11.1) | protein | 308 | 39% helix, 18% strand | Q86Y07 |
| B | SERINE/THREONINE-protein kinase VRK2 (EC 2.7.11.1) | protein | 287 | 39% helix, 19% strand | Q86Y07 |
Ligands and binding sites
- KJD · 4-[6-amino-5-(3,5-difluoro-4-hydroxyphenyl)pyridin-3-yl]benzene-1-sulfonamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.66 | 0.80 | 40 | KJD |
| 2 | 286 | 0.64 | 0.81 | 26 | KJD |
| 3 | 247 | 0.56 | 0.77 | 31 | empty |
| 4 | 81 | 0.43 | 0.80 | 14 | empty |
| 5 | 128 | 0.39 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 154 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6NCG · Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- Q86Y07 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase VRK2 (Q86Y07) · 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 Q86Y07
- Elsewhere: RCSB PDB 6NCG · PDBe 6NCG · UniProt Q86Y07
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