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Phosphoinositide-dependent kinase-1 (PDK1) kinase domain with 1,1- DIMETHYLETHYL{(3R,5R)-1-[2-amino-6-(3-amino-1H-indazol-6-yl)-4- pyrimidinyl]-5-methyl-3-PIPERIDINYL}CARBAMATE
Analyse Phosphoinositide-dependent kinase-1 (PDK1) kinase domain with 1,1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QD4
- Type
- protein
- Length
- 276 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
- 3Q6, SO4
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) | protein | 276 | 40% helix, 17% strand | O15530 |
Ligands and binding sites
- 3Q6 · tert-butyl {(3R,5R)-1-[2-amino-6-(3-amino-2H-indazol-6-yl)pyrimidin-4-yl]-5-methylpiperidin-3-yl}carbamate · ligand · chains A
- SO4 · Sulfate ion · ion · 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 | 374 | 0.66 | 0.80 | 38 | 3Q6 |
| 2 | 53 | 0.40 | 0.82 | 17 | empty |
Compared structures
- 3QD4 · Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with… · 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 3QD4 · PDBe 3QD4 · UniProt O15530
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