Research workbench
Crystal structure of polo-like kinase 1 in complex with nms-P937
Analyse Crystal structure of polo-like kinase 1 in complex with nms-P937 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YAC
- Type
- protein
- Length
- 290 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
- 937, ZN
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 290 | 35% helix, 19% strand | P53350 |
Ligands and binding sites
- 937 · 1-(2-hydroxyethyl)-8-[[5-(4-methylpiperazin-1-yl)-2-(trifluoromethoxy)phenyl]amino]-4,5-dihydropyrimido[5,4-g]indazole-3-carboxamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- TLA · L(+)-tartaric acid · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.65 | 0.82 | 31 | 937 |
| 2 | 148 | 0.51 | 0.79 | 21 | empty |
| 3 | 96 | 0.41 | 0.77 | 23 | empty |
| 4 | 69 | 0.31 | 0.75 | 15 | empty |
| 5 | 53 | 0.29 | 0.75 | 9 | empty |
Compared structures
- 2YAC · Crystal structure of Polo-like kinase 1 in complex with NMS-P937 · the same entry in another collection · chain A against A, TM-score 1.00
- P53350 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase PLK1 (P53350) · a predicted model of the same protein · 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 2YAC · PDBe 2YAC · UniProt P53350
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