SMTL ID : 2pe1.1

CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) {2-Oxo-3-[1-(1H-pyrrol-2-yl)-eth-(Z)-ylidene]-2,3-dihydro-1H-indol-5-yl}-urea {BX-517} COMPLEX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: K.3, R.58, T.75, F.76, Q.77 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.75, A:Q.77, A:Q.77 Water bridges: A:R.58, A:R.58 Salt bridges: A:K.3, A:R.58 SO4.2: 1 residues within 4Å: Chain A: R.33 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.33

1 x 517: 1-{2-OXO-3-[(1R)-1-(1H-PYRROL-2-YL)ETHYL]-2H-INDOL-5-YL}UREA(Non-covalent)

517.3: 12 residues within 4Å: Chain A: L.15, V.23, A.36, K.38, L.86, S.87, Y.88, A.89, G.92, L.139, T.149, D.150 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.15, A:L.86, A:L.139 Hydrogen bonds: A:K.38, A:S.87, A:A.89, A:D.150, A:D.150, A:D.150 Water bridges: A:T.149

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: G.18, S.19, F.20, S.21 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.19, A:F.20, A:S.21, A:S.21 GOL.5: 2 residues within 4Å: Chain A: F.9, F.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.11 GOL.6: 2 residues within 4Å: Chain A: F.11, K.81 No protein-ligand interaction detected (PLIP) GOL.7: 6 residues within 4Å: Chain A: S.21, K.38, L.40, Y.53, E.57 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.21, A:K.38, A:K.38 Water bridges: A:D.150, A:G.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Islam, I. et al., Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 1: Design, synthesis and biological activity. Bioorg.Med.Chem.Lett. (2007)

Release Date

2007-06-12

Peptides

3-phosphoinositide-dependent protein kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3-phosphoinositide-dependent protein kinase 1

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