MolNFT v1 · #167864 · protein
Structure of human vaccinia-related kinase 1 (VRK1) bound to ACH471
6VXU · SERINE/THREONINE-protein kinase VRK1: “Structure of human vaccinia-related kinase 1 (VRK1) bound to ACH471”. X-ray diffraction, 3 ligands (RTJ, VBD, SO4), 12 pockets (best druggability 0.70). MolNFT v1 #167864 on GenesisL1: 3D…
- PDB
- 6VXU
- Type
- protein
- Length
- 1,251 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
- RTJ, VBD, SO4
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 320 | 39% helix, 19% strand | Q99986 |
| B | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 305 | 42% helix, 16% strand | Q99986 |
| C | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 311 | 41% helix, 17% strand | Q99986 |
| D | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 315 | 41% helix, 17% strand | Q99986 |
Ligands and binding sites
- RTJ · (7R)-8-(cyclopropylmethyl)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one · ligand · 3 copies · chains A, B, D
- VBD · (7S)-8-(cyclopropylmethyl)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one · ligand · chains C
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.70 | 0.78 | 68 | SO4 |
| 2 | 655 | 0.69 | 0.77 | 73 | empty |
| 3 | 276 | 0.61 | 0.79 | 32 | RTJ |
| 4 | 58 | 0.60 | 0.91 | 22 | empty |
| 5 | 163 | 0.56 | 0.80 | 21 | RTJ |
Interfaces
2 interfaces between chains.
- C–D · 212 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 185 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6VXU · Structure of Human Vaccinia-related Kinase 1 (VRK1) bound to ACH471 · 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 6VXU · PDBe 6VXU · UniProt Q99986
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