MolNFT v1 · #17179 · protein
Structure of human PDK1 kinase domain in complex with staurosporine
1OKY · 3-phosphoinositide dependent protein kinase 1: “Structure of human PDK1 kinase domain in complex with staurosporine”. X-ray diffraction, 2 ligands (STU, SO4), 3 pockets (best druggability 0.63). MolNFT v1 #17179 on GenesisL1: 3D…
- PDB
- 1OKY
- Type
- protein
- Length
- 282 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-phosphoinositide dependent protein kinase 1
- EC
- 2.7.1.37
- UniProt
- O15530
- Ligands
- STU, SO4
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoinositide dependent protein kinase 1 (EC 2.7.1.37) | protein | 282 | 40% helix, 18% strand | O15530 |
Ligands and binding sites
- STU · Staurosporine · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- GOL · Glycerol · additive · 3 copies · 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 | 223 | 0.63 | 0.82 | 25 | STU |
| 2 | 110 | 0.45 | 0.79 | 22 | empty |
| 3 | 51 | 0.24 | 0.72 | 13 | GOL |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 1OKY · Structure of human PDK1 kinase domain in complex with staurosporine · the same entry in another collection · chain A against A, TM-score 1.00
- O15530 · AlphaFold monomer V2.0 prediction for 3-phosphoinositide-dependent protein kinase 1… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O15530
- Elsewhere: RCSB PDB 1OKY · PDBe 1OKY · UniProt O15530
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