MolNFT v1 · #72516 · protein

PDK1 in complex with inhibitor MP7

3NAX · 3-phosphoinositide-dependent protein kinase 1: “PDK1 in complex with inhibitor MP7”. X-ray diffraction, 1 ligand (MP7), 3 pockets (best druggability 0.77). MolNFT v1 #72516 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3NAX
Type: protein
Length: 278 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: MP7
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1)	protein	278	39% helix, 19% strand	O15530

Ligands and binding sites

MP7 · 1-(3,4-difluorobenzyl)-2-oxo-N-{(1R)-2-[(2-oxo-2,3-dihydro-1H-benzimidazol-5-yl)oxy]-1-phenylethyl}-1,2-dihydropyridine-3-carboxamide · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 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	259	0.77	0.90	40	MP7
2	75	0.39	0.78	24	empty
3	63	0.28	0.73	16	empty

Compared structures

3NAX · PDK1 in complex with inhibitor MP7 · 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 3NAX · PDBe 3NAX · UniProt O15530

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