MolNFT v1 · #136470 · protein
Crystal structure of human vaccinia-related kinase 2 (vrk-2) bound to bi-D1870
5UU1 · SERINE/THREONINE-protein kinase VRK2: “Crystal structure of human vaccinia-related kinase 2 (vrk-2) bound to bi-D1870”. X-ray diffraction, 1 ligand (7DZ), 3 pockets (best druggability 0.59). MolNFT v1 #136470 on GenesisL1: 3D…
- PDB
- 5UU1
- Type
- protein
- Length
- 315 residues
- Chains
- 1
- 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
- 7DZ
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase VRK2 (EC 2.7.11.1) | protein | 315 | 38% helix, 19% strand | Q86Y07 |
Ligands and binding sites
- 7DZ · (7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.59 | 0.82 | 23 | 7DZ |
| 2 | 65 | 0.36 | 0.78 | 15 | empty |
| 3 | 53 | 0.31 | 0.76 | 14 | empty |
Compared structures
- 5UU1 · Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to BI-D1870 · 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 5UU1 · PDBe 5UU1 · UniProt Q86Y07
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