SMTL ID : 3qd0.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: R.59, E.60, Y.61, Y.99, S.113, Y.114 Ligands: SO4.9, SO4.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.59, A:Y.114 GOL.2: 3 residues within 4Å: Chain A: E.147, G.287, K.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.147, A:K.290 GOL.3: 3 residues within 4Å: Chain A: E.281, E.284, G.285 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.284 GOL.4: 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:S.144, A:L.303, A:H.304 Water bridges: A:S.144, A:E.147 GOL.11: 8 residues within 4Å: Chain A: F.46, S.47, K.64, L.66, Y.79, V.80, E.83 Ligands: 3Q4.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.47, A:K.64

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

SO4.5: 4 residues within 4Å: Chain A: V.298, T.299, W.300, E.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.300, A:E.301 SO4.6: 2 residues within 4Å: Chain A: R.89, K.152 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.89, A:K.152 SO4.7: 5 residues within 4Å: Chain A: K.29, R.84, T.101, F.102, Q.103 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.101, A:T.101, A:Q.103 Salt bridges: A:K.29, A:R.84 SO4.9: 4 residues within 4Å: Chain A: Y.99, S.113, Q.173 Ligands: GOL.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.99, A:S.113 SO4.10: 2 residues within 4Å: Chain A: R.59 Ligands: GOL.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.59

1 x 3Q4: (3S,6R)-1-[2-amino-6-(3-amino-2H-indazol-6-yl)pyrimidin-4-yl]-6-methyl-N-phenylpiperidine-3-carboxamide(Non-covalent)

3Q4.8: 20 residues within 4Å: Chain A: L.41, E.43, G.44, S.47, V.49, A.62, K.64, Y.79, E.83, M.87, L.112, S.113, Y.114, A.115, L.165, T.175, D.176, G.178, T.179 Ligands: GOL.11 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.49, A:Y.79, A:Y.79, A:L.165, A:T.179 Hydrogen bonds: A:K.64, A:K.64, A:A.115, A:A.115, A:A.115, A:D.176, A:D.176 Water bridges: A:D.176 Salt bridges: A:E.83

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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