Research workbench
Structure of PLK1 kinase domain in complex with a benzolactam-derived inhibitor
Analyse Structure of PLK1 kinase domain in complex with a benzolactam-derived inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3THB
- Type
- protein
- Length
- 287 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
- 3TA, ZN
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 287 | 34% helix, 20% strand | P53350 |
Ligands and binding sites
- 3TA · 9-chloro-2-({5-[3-(dimethylamino)propyl]-2-methylpyridin-3-yl}amino)-5,7-dihydro-6H-pyrimido[5,4-d][1]benzazepine-6-thi one · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.71 | 0.82 | 45 | 3TA |
| 2 | 68 | 0.50 | 0.84 | 18 | empty |
| 3 | 125 | 0.47 | 0.78 | 22 | empty |
| 4 | 94 | 0.37 | 0.76 | 16 | empty |
| 5 | 51 | 0.29 | 0.75 | 10 | empty |
Compared structures
- 3THB · Structure of PLK1 kinase domain in complex with a benzolactam-derived inhibitor · 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 3THB · PDBe 3THB · UniProt P53350
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