MolNFT v1 · #63515 · protein
PLK1 in complex with BI6727
3FC2 · SERINE/THREONINE-protein kinase PLK1: “PLK1 in complex with BI6727”. X-ray diffraction, 2 ligands (IBI, ZN), 3 pockets (best druggability 0.72). MolNFT v1 #63515 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3FC2
- 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
- IBI, ZN
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 293 | 35% helix, 20% strand | P53350 |
Ligands and binding sites
- IBI · N-{trans-4-[4-(cyclopropylmethyl)piperazin-1-yl]cyclohexyl}-4-{[(7R)-7-ethyl-5-methyl-8-(1-methylethyl)-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxybenzamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- GOL · Glycerol · additive · 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 | 539 | 0.72 | 0.80 | 49 | IBI, EDO, ACT, GOL |
| 2 | 102 | 0.47 | 0.80 | 22 | EDO |
| 3 | 83 | 0.34 | 0.75 | 18 | empty |
Compared structures
- 3FC2 · PLK1 in complex with BI6727 · 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 3FC2 · PDBe 3FC2 · UniProt P53350
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