MolNFT v1 · #93775 · protein
Human PLK1-pbd in complex with thymoquinone at the phophopeptide binding site
4HCO · SERINE/THREONINE-protein kinase PLK1: “Human PLK1-pbd in complex with thymoquinone at the phophopeptide binding site”. X-ray diffraction, 1 ligand (IMW), 5 pockets (best druggability 0.63). MolNFT v1 #93775 on GenesisL1: 3D…
- PDB
- 4HCO
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- 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
- IMW
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 220 | 33% helix, 30% strand | P53350 |
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 220 | 27% helix, 30% strand | P53350 |
Ligands and binding sites
- IMW · 2-methyl-5-(1-methylethyl)cyclohexa-2,5-diene-1,4-dione · ligand · chains A
- GOL · Glycerol · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.63 | 0.79 | 39 | empty |
| 2 | 122 | 0.47 | 0.78 | 20 | empty |
| 3 | 51 | 0.41 | 0.82 | 15 | empty |
| 4 | 124 | 0.40 | 0.75 | 20 | GOL, IMW |
| 5 | 88 | 0.32 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- B–A · 336 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4HCO · Human Plk1-PBD in complex with Thymoqui at the phophopeptide binding site · the same entry in another collection · chain B against B, 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 4HCO · PDBe 4HCO · UniProt P53350
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