SMTL ID : 2xck.1

Crystal structure of PDK1 in complex with a pyrazoloquinazoline inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x MH4: 1-METHYL-8-{[4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}-N-[(2-METHYLPYRIDIN-4-YL)METHYL]-4,5-DIHYDRO-1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE(Non-covalent)

MH4.1: 17 residues within 4Å: Chain A: L.38, G.39, E.40, G.41, S.44, T.45, T.46, A.59, K.61, L.109, S.110, Y.111, A.112, G.115, L.162, T.172, D.173 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.38, A:A.59, A:L.109, A:L.162 Hydrogen bonds: A:S.44, A:T.46, A:K.61, A:A.112, A:A.112 pi-Cation interactions: A:K.61 MH4.9: 17 residues within 4Å: Chain B: L.38, G.39, E.40, G.41, S.44, T.45, T.46, A.59, K.61, L.109, S.110, Y.111, A.112, G.115, L.162, T.172, D.173 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.38, B:A.59, B:L.109, B:L.162 Hydrogen bonds: B:S.44, B:K.61, B:A.112, B:A.112, B:T.172 pi-Cation interactions: B:K.61

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: A.53, T.54, S.55 Chain B: H.89, S.141, W.297, E.298, N.299, L.300, H.301 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.141, B:L.300, B:H.301, B:H.301, A:A.53 GOL.3: 3 residues within 4Å: Chain A: F.32, K.33, F.34 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.32, A:K.33, A:K.33, A:F.34 GOL.4: 8 residues within 4Å: Chain A: R.56, E.57, Y.96, S.110, Y.111 Ligands: SO4.7, SO4.8, GOL.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.56, A:Y.111 GOL.5: 6 residues within 4Å: Chain A: H.301, Q.302 Chain B: R.56, E.57 Ligands: GOL.12, SO4.16 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.302, B:E.57, B:E.57 GOL.10: 10 residues within 4Å: Chain A: H.89, S.141, W.297, E.298, N.299, L.300, H.301 Chain B: A.53, T.54, S.55 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:A.53, A:S.141, A:L.300, A:H.301, A:H.301 GOL.11: 3 residues within 4Å: Chain B: F.32, K.33, F.34 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.32, B:K.33, B:K.33, B:F.34 GOL.12: 8 residues within 4Å: Chain B: R.56, E.57, Y.96, S.110, Y.111 Ligands: GOL.5, SO4.15, SO4.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.56, B:Y.111 GOL.13: 6 residues within 4Å: Chain A: R.56, E.57 Chain B: H.301, Q.302 Ligands: GOL.4, SO4.8 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.302, A:E.57, A:E.57

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

SO4.6: 5 residues within 4Å: Chain A: K.26, R.81, T.98, F.99, Q.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.100 Salt bridges: A:K.26, A:R.81 SO4.7: 6 residues within 4Å: Chain A: K.94, Y.96 Chain B: K.94, Y.96 Ligands: GOL.4, SO4.15 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.96 Salt bridges: A:K.94, B:K.94 SO4.8: 5 residues within 4Å: Chain A: R.56 Chain B: P.90, H.301 Ligands: GOL.4, GOL.13 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.56, B:H.301 SO4.14: 5 residues within 4Å: Chain B: K.26, R.81, T.98, F.99, Q.100 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.98, B:Q.100 Salt bridges: B:K.26, B:R.81 SO4.15: 6 residues within 4Å: Chain A: K.94, Y.96 Chain B: K.94, Y.96 Ligands: SO4.7, GOL.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.96 Salt bridges: A:K.94, B:K.94 SO4.16: 5 residues within 4Å: Chain A: P.90, H.301 Chain B: R.56 Ligands: GOL.5, GOL.12 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:H.301, B:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Angiolini, M. et al., Structure-Based Optimization of Potent Pdk1 Inhibitors. Bioorg.Med.Chem.Lett. (2010)

Release Date

2010-07-28

Peptides

3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1