MolNFT v1 · #76186 · protein
Phosphoinositide-dependent kinase-1 (PDK1) kinase domain with (2R,5S)- 1-[2-amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-6-methyl-N- phenyl-3-piperidinecarboxamide
3QD0 · 3-phosphoinositide-dependent protein kinase 1: “Phosphoinositide-dependent kinase-1 (PDK1) kinase domain with (2R,5S)…”. X-ray diffraction, 2 ligands (3Q4, SO4), 1 pocket (best druggability 0.67). MolNFT v1 #76186 on GenesisL1: 3D…
- PDB
- 3QD0
- Type
- protein
- Length
- 274 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
- 3Q4, SO4
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) | protein | 274 | 42% helix, 18% strand | O15530 |
Ligands and binding sites
- 3Q4 · (3S,6R)-1-[2-amino-6-(3-amino-2H-indazol-6-yl)pyrimidin-4-yl]-6-methyl-N-phenylpiperidine-3-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket 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 | 39 | 3Q4, GOL |
Compared structures
- 3QD0 · 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 3QD0 · PDBe 3QD0 · UniProt O15530
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