MolNFT v1 · #145389 · protein
Crystal structure of the human vaccinia-related kinase bound to a N,N- dipropynyl-dihydropteridine inhibitor
6CMM · SERINE/THREONINE-protein kinase VRK1: “Crystal structure of the human vaccinia-related kinase bound to a N,N- dipropynyl-dihydropteridine inhibitor”. X-ray diffraction, 2 ligands (F7D, SO4), 16 pockets (best druggability 0.71).…
- PDB
- 6CMM
- Type
- protein
- Length
- 1,259 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
- F7D, SO4
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 318 | 39% helix, 18% strand | Q99986 |
| B | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 310 | 41% helix, 18% strand | Q99986 |
| C | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 316 | 41% helix, 18% strand | Q99986 |
| D | SERINE/THREONINE-protein kinase VRK1 (EC 2.7.11.1) | protein | 315 | 41% helix, 20% strand | Q99986 |
Ligands and binding sites
- F7D · (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one · ligand · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 6 copies · chains B, C, D
- ACT · Acetate ion · additive · 8 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
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 | 787 | 0.71 | 0.77 | 80 | SO4, PEG |
| 2 | 702 | 0.71 | 0.78 | 66 | empty |
| 3 | 218 | 0.58 | 0.79 | 29 | F7D |
| 4 | 240 | 0.57 | 0.78 | 34 | empty |
| 5 | 185 | 0.55 | 0.79 | 27 | F7D |
Interfaces
2 interfaces between chains.
- A–B · 208 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 205 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6CMM · Crystal Structure of the Human vaccinia-related kinase bound to a… · 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 6CMM · PDBe 6CMM · UniProt Q99986
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