Research workbench
Structure of human PDK1 kinase domain in complex with LY333531
Analyse Structure of human PDK1 kinase domain in complex with LY333531 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UU3
- Type
- protein
- Length
- 277 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
- LY4, SO4
- Pockets
- 3 · best druggability 0.67
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 | 277 | 40% helix, 18% strand | O15530 |
Ligands and binding sites
- LY4 · (9R)-9-[(dimethylamino)methyl]-6,7,10,11-tetrahydro-9H,18H-5,21:12,17-dimethenodibenzo[e,k]pyrrolo[3,4-h][1,4,13]oxadia zacyclohexadecine-18,20-dione · ligand · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A
- GOL · Glycerol · additive · 8 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 | 439 | 0.67 | 0.79 | 36 | GOL, SO4, LY4 |
| 2 | 110 | 0.36 | 0.73 | 23 | GOL, SO4 |
| 3 | 57 | 0.30 | 0.75 | 15 | SO4 |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 1UU3 · Structure of human PDK1 kinase domain in complex with LY333531 · 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 0.99
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 1UU3 · PDBe 1UU3 · UniProt O15530
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