SMTL ID : 1uu3.1

Structure of human PDK1 kinase domain in complex with LY333531

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: R.56, E.57, Y.58, Y.96, S.110, Y.111 Ligands: SO4.10, SO4.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.56, A:Y.111 Water bridges: A:E.57, A:E.57 GOL.2: 7 residues within 4Å: Chain A: S.44, K.61, L.63, Y.76, V.77, E.80 Ligands: SO4.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.44, A:S.44, A:K.61 GOL.3: 4 residues within 4Å: Chain A: P.29, I.62, K.104, Y.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.104, A:K.104 GOL.4: 4 residues within 4Å: Chain A: K.26, R.81, F.97, T.98 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.25, A:R.81, A:T.98, A:T.98 Water bridges: A:K.27 GOL.5: 4 residues within 4Å: Chain A: L.247, Y.249, F.251, R.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.247 Water bridges: A:R.260 GOL.6: 7 residues within 4Å: Chain A: H.89, S.141, W.297, E.298, N.299, L.300, H.301 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.141, A:L.300, A:H.301, A:H.301 Water bridges: A:S.141 GOL.7: 3 residues within 4Å: Chain A: F.32, K.33, F.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.34 Water bridges: A:F.32 GOL.8: 3 residues within 4Å: Chain A: G.39, E.40 Ligands: LY4.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.40 Water bridges: A:E.116, A:E.116

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

SO4.9: 5 residues within 4Å: Chain A: K.26, R.81, T.98, F.99, Q.100 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.100 Water bridges: A:R.81, A:R.81, A:R.81, A:F.99, A:Q.100 Salt bridges: A:K.26, A:R.81 SO4.10: 4 residues within 4Å: Chain A: Y.96, S.110, Q.170 Ligands: GOL.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.96, A:S.110 Water bridges: A:Y.111, A:Y.111, A:Q.170 SO4.11: 2 residues within 4Å: Chain A: R.56 Ligands: GOL.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.56 Salt bridges: A:R.56 SO4.12: 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 SO4.13: 6 residues within 4Å: Chain A: G.41, S.42, F.43, S.44 Ligands: GOL.2, LY4.16 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.42, A:F.43, A:S.44, A:S.44 Water bridges: A:S.44, A:S.44 Salt bridges: A:K.61 SO4.14: 2 residues within 4Å: Chain A: R.86, K.149 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.86, A:K.149 SO4.15: 2 residues within 4Å: Chain A: H.301, Q.302 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.302 Water bridges: A:H.301, A:H.301 Salt bridges: A:H.301

1 x LY4: (9R)-9-[(DIMETHYLAMINO)METHYL]-6,7,10,11-TETRAHYDRO-9H,18H-5,21:12,17-DIMETHENODIBENZO[E,K]PYRROLO[3,4-H][1,4,13]OXADIA ZACYCLOHEXADECINE-18,20-DIONE(Non-covalent)

LY4.16: 20 residues within 4Å: Chain A: L.38, G.39, G.41, A.59, K.61, E.80, V.93, L.109, S.110, Y.111, A.112, G.115, E.116, E.159, N.160, L.162, T.172, D.173 Ligands: GOL.8, SO4.13 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.38, A:K.61, A:L.109, A:E.159, A:L.162, A:T.172, A:D.173 Hydrogen bonds: A:S.110, A:A.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Komander, D. et al., Interactions of Ly333531 and Other Bisindolyl Maleimide Inhibitors with Pdk1. Structure (2004)

Release Date

2004-03-04

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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