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Crystal structure of an activated (Thr->Asp) Polo-like kinase 1 (Plk1) catalytic domain in complex with Compound 902
Analyse Crystal structure of an activated (Thr->Asp) Polo-like kinase 1 (Plk1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DB6
- Type
- protein
- Length
- 287 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.85
- Source
- Danio rerio
- Molecule
- Polo-like kinase 1
- EC
- 2.7.11.21
- UniProt
- Q4KMI8
- Ligands
- FRS
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.85 · 1 distinct chain · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polo-like kinase 1 (EC 2.7.11.21) | protein | 287 | 34% helix, 20% strand | Q4KMI8 |
Ligands and binding sites
- FRS · 1-[5-methyl-2-(trifluoromethyl)furan-3-yl]-3-[(2Z)-5-(2-{[6-(1H-1,2,4-triazol-3-ylamino)pyrimidin-4-yl]amino}ethyl)-1,3-thiazol-2(3H)-ylidene]urea · ligand · 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 | 491 | 0.71 | 0.80 | 42 | FRS |
| 2 | 95 | 0.42 | 0.78 | 22 | empty |
| 3 | 51 | 0.28 | 0.75 | 13 | empty |
Compared structures
- 3DB6 · Crystal structure of an activated (thr->asp) polo-like kinase 1 (PLK1) catalytic domain… · 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 Q4KMI8
- Elsewhere: RCSB PDB 3DB6 · PDBe 3DB6 · UniProt Q4KMI8
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