Research workbench
Crystal structure of PLK4 kinase with an inhibitor: 400631 ((1R,2S)-2- {3-[(E)-2-{4-[(DIMETHYLAMINO)METHYL]PHENYL}ETHENYL]-2H-indazol-6-yl}- 5'-METHOXYSPIRO[CYCLOPROPANE-1,3'-indol]-2'(1'H)-one)
Analyse Crystal structure of PLK4 kinase with an inhibitor: 400631 ((1R,2S)-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JXF
- Type
- protein
- Length
- 235 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PLK4
- EC
- 2.7.11.21
- UniProt
- O00444
- Ligands
- 631
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK4 (EC 2.7.11.21) | protein | 235 | 39% helix, 17% strand | O00444 |
Ligands and binding sites
- 631 · (1R,2S)-2-{3-[(E)-2-{4-[(dimethylamino)methyl]phenyl}ethenyl]-2H-indazol-6-yl}-5'-methoxyspiro[cyclopropane-1,3'-indol]-2'(1'H)-one · ligand · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · 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 | 218 | 0.68 | 0.85 | 31 | 631, EDO |
| 2 | 68 | 0.37 | 0.78 | 17 | empty |
| 3 | 64 | 0.31 | 0.75 | 15 | empty |
Compared structures
- 4JXF · Crystal Structure of PLK4 Kinase with an inhibitor: 400631… · the same entry in another collection · chain A against A, TM-score 1.00
- O00444 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase PLK4 (O00444) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 O00444
- Elsewhere: RCSB PDB 4JXF · PDBe 4JXF · UniProt O00444
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