SMTL ID : 2xch.1

Crystal structure of PDK1 in complex with a pyrazoloquinazoline inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x CKG: 8-(CYCLOHEXA-2,5-DIEN-1-YLIDENEAMINO)-1-(PIPERIDIN-4-YLMETHYL)-4,5-DIHYDRO-1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE(Non-covalent)

CKG.1: 17 residues within 4Å: Chain A: L.38, G.39, V.46, A.59, K.61, L.109, S.110, Y.111, A.112, K.113, G.115, E.116, E.159, L.162, T.172, D.173 Ligands: GOL.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.38, A:A.59, A:L.109, A:Y.111, A:L.162, A:L.162, A:T.172 Hydrogen bonds: A:K.61, A:A.112, A:E.116, A:E.159, A:D.173 Water bridges: A:E.80 CKG.14: 17 residues within 4Å: Chain B: L.38, G.39, V.46, A.59, K.61, L.109, S.110, Y.111, A.112, K.113, G.115, E.116, E.159, L.162, T.172, D.173 Ligands: GOL.19 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.38, B:A.59, B:L.109, B:Y.111, B:L.162, B:L.162, B:T.172 Hydrogen bonds: B:K.61, B:A.112, B:E.159, B:D.173 Water bridges: B:K.61

12 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.32, A:F.34 GOL.4: 9 residues within 4Å: Chain A: R.56, E.57, Y.58, Y.96, S.110, Y.111 Ligands: SO4.9, SO4.10, GOL.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.56, A:Y.111 Water bridges: A:Y.58 GOL.5: 6 residues within 4Å: Chain A: H.301, Q.302 Chain B: R.56, E.57 Ligands: GOL.17, SO4.23 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.6: 7 residues within 4Å: Chain A: G.41, S.42, F.43, S.44, K.61, D.173 Ligands: CKG.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.42, A:S.42, A:F.43, A:S.44, A:K.61, A:D.173 GOL.7: 4 residues within 4Å: Chain A: L.247, Y.249, F.251, R.260 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.251, A:F.251 GOL.15: 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 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.141, A:L.300, A:H.301, A:H.301, B:A.53 Water bridges: A:E.144 GOL.16: 3 residues within 4Å: Chain B: F.32, K.33, F.34 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.32, B:F.34 GOL.17: 9 residues within 4Å: Chain B: R.56, E.57, Y.58, Y.96, S.110, Y.111 Ligands: GOL.5, SO4.22, SO4.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.56, B:Y.111 GOL.18: 6 residues within 4Å: Chain A: R.56, E.57 Chain B: H.301, Q.302 Ligands: GOL.4, SO4.10 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.302, A:E.57, A:E.57 GOL.19: 7 residues within 4Å: Chain B: G.41, S.42, F.43, S.44, K.61, D.173 Ligands: CKG.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.42, B:S.42, B:F.43, B:S.44, B:K.61, B:D.173 GOL.20: 4 residues within 4Å: Chain B: L.247, Y.249, F.251, R.260 2 PLIP interactions: 2 interactions with chain B Water bridges: B:F.251, B:F.251

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

SO4.8: 5 residues within 4Å: Chain A: K.26, R.81, T.98, F.99, Q.100 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.100 Water bridges: A:K.26, A:R.81, A:R.81, A:Q.100 Salt bridges: A:K.26, A:R.81 SO4.9: 6 residues within 4Å: Chain A: Y.96, S.110, Y.111, Q.170 Ligands: GOL.4, SO4.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.96, A:S.110, A:Q.170 Water bridges: A:Y.111 SO4.10: 6 residues within 4Å: Chain A: R.56 Chain B: P.90, H.301 Ligands: GOL.4, GOL.18, SO4.26 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:R.56 Salt bridges: A:R.56, B:H.301 SO4.11: 4 residues within 4Å: Chain A: V.295, T.296, W.297, E.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.297, A:E.298 SO4.12: 5 residues within 4Å: Chain A: Q.23, P.24, R.25 Chain B: R.86, K.149 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.86, B:K.149, A:R.25 Hydrogen bonds: A:Q.23, A:R.25 SO4.13: 7 residues within 4Å: Chain A: K.94, Y.96 Chain B: K.94, Y.96 Ligands: SO4.9, SO4.23, SO4.26 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.96, A:Y.96 Water bridges: B:Y.96 Salt bridges: B:K.94, A:K.94 SO4.21: 5 residues within 4Å: Chain B: K.26, R.81, T.98, F.99, Q.100 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.98, B:Q.100 Water bridges: B:K.26, B:R.81, B:R.81, B:Q.100 Salt bridges: B:K.26, B:R.81 SO4.22: 6 residues within 4Å: Chain B: Y.96, S.110, Y.111, Q.170 Ligands: GOL.17, SO4.26 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.96, B:Y.96, B:S.110, B:Q.170 Water bridges: B:Y.111 SO4.23: 6 residues within 4Å: Chain A: P.90, H.301 Chain B: R.56 Ligands: GOL.5, SO4.13, GOL.17 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:H.301, B:R.56 Water bridges: B:R.56 SO4.24: 4 residues within 4Å: Chain B: V.295, T.296, W.297, E.298 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.297, B:E.298, B:E.298 SO4.25: 5 residues within 4Å: Chain A: R.86, K.149 Chain B: Q.23, P.24, R.25 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.86, A:K.149, B:R.25 Hydrogen bonds: B:Q.23, B:R.25 SO4.26: 7 residues within 4Å: Chain A: K.94, Y.96 Chain B: K.94, Y.96 Ligands: SO4.10, SO4.13, SO4.22 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.96, A:Y.96 Salt bridges: A:K.94, B:K.94 Water bridges: 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

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