Research workbench
Human PDK1 kinase domain in complex with allosteric compound PS182 bound to the pif-pocket
Analyse Human PDK1 kinase domain in complex with allosteric compound PS182 bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AW0
- Type
- protein
- Length
- 285 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-phosphoinositide-dependent protein kinase 1
- EC
- 2.7.11.1
- UniProt
- O15530
- Ligands
- ATP, MJF, MG
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) | protein | 285 | 40% helix, 19% strand | O15530 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MJF · [(1R)-3-(4-chlorophenyl)-3-oxo-1-phenylpropyl]propanedioic acid · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
- DTD · Dithiane diol · additive · 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 | 387 | 0.67 | 0.80 | 37 | ATP, MG |
| 2 | 53 | 0.34 | 0.78 | 10 | MJF |
Modifications
Observed in the structure: 2 modified (artifact, phosphorylation).
Compared structures
- 4AW0 · Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the PIF-Pocket · 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 O15530
- Elsewhere: RCSB PDB 4AW0 · PDBe 4AW0 · UniProt O15530
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