Research workbench
Phosphoinositide-dependent kinase-1 (PDK1) with FRAGMENT17
Analyse Phosphoinositide-dependent kinase-1 (PDK1) with FRAGMENT17 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NUY
- Type
- protein
- Length
- 277 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pkb-like
- UniProt
- Q9UPJ8
- Ligands
- JPZ, SO4
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pkb-like | protein | 277 | 42% helix, 17% strand | Q9UPJ8 |
Ligands and binding sites
- JPZ · quinazolin-4(1H)-one · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.67 | 0.80 | 37 | JPZ |
| 2 | 75 | 0.30 | 0.73 | 21 | GOL |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3NUY · phosphoinositide-dependent kinase-1 (PDK1) with fragment17 · 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 Q9UPJ8
- Elsewhere: RCSB PDB 3NUY · PDBe 3NUY · UniProt Q9UPJ8
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