MolNFT v1 · #95933 · protein
Crystal structure of PLK1 in complex with tak-960
4J53 · SERINE/THREONINE-protein kinase PLK1: “Crystal structure of PLK1 in complex with tak-960”. X-ray diffraction, 2 ligands (1J4, ZN), 4 pockets (best druggability 0.65). MolNFT v1 #95933 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4J53
- Type
- protein
- Length
- 293 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PLK1
- EC
- 2.7.11.21
- UniProt
- P53350
- Ligands
- 1J4, ZN
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 293 | 34% helix, 19% strand | P53350 |
Ligands and binding sites
- 1J4 · 4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino]-2-fluoro-5-methoxy-N-(1-methylpiperidin-4-yl)benzamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.65 | 0.82 | 33 | 1J4 |
| 2 | 156 | 0.51 | 0.78 | 18 | empty |
| 3 | 110 | 0.45 | 0.78 | 22 | ACT |
| 4 | 80 | 0.35 | 0.76 | 18 | empty |
Compared structures
- 4J53 · Crystal structure of PLK1 in complex with TAK-960 · 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 P53350
- Elsewhere: RCSB PDB 4J53 · PDBe 4J53 · UniProt P53350
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