Research workbench
Crystal structure of PLK1 in complex with a novel 5,6- DIHYDROIMIDAZOLO[1,5-F]PTERIDINE inhibitor
Analyse Crystal structure of PLK1 in complex with a novel 5,6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TA8
- Type
- protein
- Length
- 294 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
- 79C, ZN
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 294 | 36% helix, 18% strand | P53350 |
Ligands and binding sites
- 79C · 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]-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.64 | 0.81 | 35 | 79C |
| 2 | 174 | 0.55 | 0.80 | 20 | empty |
| 3 | 102 | 0.43 | 0.78 | 26 | empty |
| 4 | 55 | 0.32 | 0.76 | 12 | empty |
| 5 | 75 | 0.32 | 0.74 | 15 | empty |
Compared structures
- 5TA8 · Crystal structure of PLK1 in complex with a novel 5,6-dihydroimidazolo[1,5-f]pteridine… · 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 5TA8 · PDBe 5TA8 · UniProt P53350
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