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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

Analyse Phosphoinositide-dependent kinase-1 (PDK1) kinase domain with (2R,5S)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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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