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Pdk-1 in complex with the inhibitor compound-8I

Analyse Pdk-1 in complex with the inhibitor compound-8I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IOP
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: 8I1
Pockets: 2 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1)	protein	276	41% helix, 18% strand	O15530

Ligands and binding sites

8I1 · 2-(5-{[(2R)-2-amino-3-phenylpropyl]oxy}pyridin-3-yl)-8,9-dimethoxybenzo[c][2,7]naphthyridin-4-amine · ligand · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	378	0.65	0.79	38	8I1
2	51	0.25	0.73	16	empty

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

3IOP · PDK-1 in complex with the inhibitor Compound-8i · 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 3IOP · PDBe 3IOP · UniProt O15530

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