SMTL ID : 3nuu.2 (1 other biounit)

phosphoinositide-dependent kinase-1 (PDK1) with fragment11

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: R.34, E.35, Y.36, Y.74, S.88, Y.89 Ligands: SO4.8, SO4.9, SO4.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.34, A:Y.89 GOL.2: 3 residues within 4Å: Chain A: E.122, G.262, K.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.122, A:K.265 GOL.3: 2 residues within 4Å: Chain A: E.259, G.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.259 Water bridges: A:Y.261 GOL.4: 10 residues within 4Å: Chain A: H.67, S.119, W.275, E.276, N.277, L.278, H.279 Chain B: A.31, T.32, S.33 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:A.31, B:T.32, B:S.33, A:S.119, A:L.278, A:H.279 GOL.16: 9 residues within 4Å: Chain B: R.34, E.35, Y.36, Y.74, S.88, Y.89 Ligands: SO4.23, SO4.24, SO4.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.34, B:Y.89 GOL.17: 3 residues within 4Å: Chain B: E.122, G.262, K.265 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.122, B:K.265 Water bridges: B:E.122 GOL.18: 2 residues within 4Å: Chain B: E.259, G.260 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.261 GOL.19: 10 residues within 4Å: Chain A: A.31, T.32, S.33 Chain B: H.67, S.119, W.275, E.276, N.277, L.278, H.279 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.31, A:T.32, A:S.33, B:S.119, B:L.278, B:H.279

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

SO4.5: 4 residues within 4Å: Chain A: V.273, T.274, W.275, E.276 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: R.64, K.127 Chain B: P.2, R.3 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: K.4, R.59, T.76, F.77, Q.78 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: R.34 Chain B: P.68, H.279 Ligands: GOL.1, SO4.12 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: Y.74, S.88, N.142 Ligands: GOL.1 Ligand excluded by PLIP SO4.10: 1 residues within 4Å: Chain A: R.238 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: L.225, Y.227, D.228, F.229 Ligand excluded by PLIP SO4.12: 6 residues within 4Å: Chain A: R.34, E.35 Chain B: H.279, Q.280 Ligands: GOL.1, SO4.8 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain A: K.11, R.28 Ligand excluded by PLIP SO4.14: 9 residues within 4Å: Chain A: G.19, S.20, F.21, S.22, K.39, L.41, Y.54, E.58, D.151 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain B: V.273, T.274, W.275, E.276 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain A: P.2, R.3 Chain B: R.64, K.127 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain B: K.4, R.59, T.76, F.77, Q.78 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain A: P.68, H.279 Chain B: R.34 Ligands: GOL.16, SO4.27 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: Y.74, S.88, N.142 Ligands: GOL.16 Ligand excluded by PLIP SO4.25: 1 residues within 4Å: Chain B: R.238 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain B: L.225, Y.227, D.228, F.229 Ligand excluded by PLIP SO4.27: 6 residues within 4Å: Chain A: H.279, Q.280 Chain B: R.34, E.35 Ligands: GOL.16, SO4.23 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain B: K.11, R.28 Ligand excluded by PLIP SO4.29: 9 residues within 4Å: Chain B: G.19, S.20, F.21, S.22, K.39, L.41, Y.54, E.58, D.151 Ligand excluded by PLIP

2 x JOZ: 3,4-dihydroisoquinolin-1(2H)-one(Non-covalent)

JOZ.15: 9 residues within 4Å: Chain A: L.16, V.24, A.37, L.87, S.88, Y.89, A.90, L.140, T.150 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.16, A:V.24, A:L.140 Hydrogen bonds: A:S.88, A:A.90 JOZ.30: 9 residues within 4Å: Chain B: L.16, V.24, A.37, L.87, S.88, Y.89, A.90, L.140, T.150 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.16, B:V.24, B:L.140 Hydrogen bonds: B:S.88, B:A.90

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. ACS Med Chem Lett (2010)

Release Date

2011-05-25

Peptides

PkB-like: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PkB-like

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