SMTL ID : 3nun.1 (1 other biounit)

phosphoinositide-dependent kinase-1 (PDK1) with lead compound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: R.40, E.41, Y.42, Y.80, S.94, Y.95 Ligands: SO4.8, SO4.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.40, A:Y.95 GOL.2: 3 residues within 4Å: Chain A: E.128, G.268, K.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.128, A:K.271 GOL.3: 2 residues within 4Å: Chain A: E.265, G.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.265 Water bridges: A:Y.267 GOL.4: 7 residues within 4Å: Chain A: H.73, S.125, W.281, E.282, N.283, L.284, H.285 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.125, A:L.284, A:H.285 Water bridges: A:S.125, A:S.125

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

SO4.5: 4 residues within 4Å: Chain A: V.279, T.280, W.281, E.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.281, A:E.282 SO4.6: 2 residues within 4Å: Chain A: R.70, K.133 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.70, A:K.133 SO4.7: 5 residues within 4Å: Chain A: K.10, R.65, T.82, F.83, Q.84 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.82, A:T.82, A:Q.84 Salt bridges: A:K.10, A:R.65 SO4.8: 2 residues within 4Å: Chain A: R.40 Ligands: GOL.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.40 Salt bridges: A:R.40 SO4.9: 5 residues within 4Å: Chain A: Y.80, S.94, Y.95, Q.154 Ligands: GOL.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.95, A:Y.95, A:Q.154 SO4.10: 4 residues within 4Å: Chain A: G.25, S.26, F.27, S.28 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.26, A:F.27, A:S.28, A:S.28, A:S.28 Water bridges: A:K.45

1 x JMZ: 6-(2-AMINOPYRIMIDIN-4-YL)-1H-INDAZOL-3-AMINE(Non-covalent)

JMZ.11: 11 residues within 4Å: Chain A: V.30, A.43, K.45, E.64, L.93, S.94, Y.95, A.96, L.146, T.156, D.157 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.30, A:L.146 Hydrogen bonds: A:K.45, A:A.96, A:A.96, A:D.157 Water bridges: A:S.28 Salt bridges: A:E.64, A:D.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Medina, J.R. et al., Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery. TO BE PUBLISHED

Release Date

2011-06-22

Peptides

PkB-like: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PkB-like

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