SMTL ID : 3qd3.1

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 1,1-Dimethylethyl {(3R,6S)-1-[2-amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-6-methyl-3-piperidinyl}carbamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x 3Q5: tert-butyl {(3R,6S)-1-[2-amino-6-(3-amino-2H-indazol-6-yl)pyrimidin-4-yl]-6-methylpiperidin-3-yl}carbamate(Non-covalent)

3Q5.1: 19 residues within 4Å: Chain A: L.41, E.43, G.44, F.46, S.47, V.49, A.62, K.64, L.66, Y.79, E.83, M.87, L.112, S.113, Y.114, A.115, L.165, T.175, D.176 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.46, A:V.49, A:L.66, A:Y.79, A:L.165, A:T.175 Hydrogen bonds: A:S.47, A:K.64, A:K.64, A:A.115, A:A.115, A:A.115, A:D.176 Water bridges: A:S.47, A:D.176, A:D.176, A:G.178 Salt bridges: A:E.83

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

SO4.2: 2 residues within 4Å: Chain A: R.59 Ligands: GOL.4 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.59

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: H.92, S.144, W.300, E.301, N.302, L.303, H.304 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.92, A:S.144, A:W.300, A:L.303, A:H.304 GOL.4: 6 residues within 4Å: Chain A: E.60, Y.61, Y.99, S.113, Y.114 Ligands: SO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.61, A:Y.114 Water bridges: A:E.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Medina, J.R. et al., Structure-Based Design of Potent and Selective 3-Phosphoinositide-Dependent Kinase-1 (PDK1) Inhibitors. J.Med.Chem. (2011)

Release Date

2011-03-09

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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