Research workbench
Crystal structure of the human vaccinia-related kinase 1 bound to an oxindole inhibitor
Analyse Crystal structure of the human vaccinia-related kinase 1 bound to an oxindole… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UKF
- Type
- protein
- Length
- 1,172 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
- 8E1, PO4, CL
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 322 | 39% helix, 18% strand | Q99986 |
| B | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 265 | 48% helix, 11% strand | Q99986 |
| C | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 317 | 40% helix, 17% strand | Q99986 |
| D | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 268 | 48% helix, 10% strand | Q99986 |
Ligands and binding sites
- 8E1 · 4-{[(Z)-(7-oxo-6,7-dihydro-8H-[1,3]thiazolo[5,4-e]indol-8-ylidene)methyl]amino}benzene-1-sulfonamide · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 7 copies · chains A, B, C
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.72 | 0.79 | 73 | empty |
| 2 | 283 | 0.68 | 0.83 | 28 | 8E1 |
| 3 | 254 | 0.67 | 0.83 | 44 | 8E1 |
| 4 | 74 | 0.66 | 0.93 | 19 | empty |
| 5 | 52 | 0.63 | 0.94 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 272 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 238 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5UKF · Crystal Structure of the Human Vaccinia-related Kinase 1 Bound to an Oxindole Inhibitor · the same entry in another collection · chain D against D, 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 B against A, TM-score 0.99
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 5UKF · PDBe 5UKF · UniProt Q99986
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.