SMTL ID : 4rqv.1

Crystal structure of PDK1 in complex with ATP and the PIF-pocket ligand RS2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: H.91, P.92, F.93, S.143, W.299, E.300, N.301, L.302, H.303, Q.304 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.91, A:E.300, A:L.302, A:H.303, A:H.303 GOL.2: 7 residues within 4Å: Chain A: R.58, E.59, Y.60, Y.98, L.111, S.112, Y.113 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.58, A:E.59, A:Y.113 Water bridges: A:R.58, A:E.59, A:Y.60, A:K.115 GOL.3: 3 residues within 4Å: Chain A: F.34, K.35, F.36 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.36, A:F.36 Water bridges: A:F.34, A:K.35 GOL.4: 5 residues within 4Å: Chain A: I.123, R.124, G.127, G.230, L.231 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.124

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 18 residues within 4Å: Chain A: L.40, G.41, E.42, G.43, S.44, S.46, V.48, A.61, K.63, V.95, L.111, S.112, Y.113, A.114, E.118, E.161, L.164, T.174 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.44, A:S.44, A:S.46, A:S.112, A:A.114, A:E.118, A:E.118 Water bridges: A:T.174 Salt bridges: A:K.63

1 x R2S: N-(6-chloro-1,3-benzothiazol-2-yl)-1-benzothiophene-2-sulfonamide(Non-covalent)

R2S.6: 13 residues within 4Å: Chain A: K.67, I.70, I.71, V.76, V.79, T.80, R.83, T.100, F.101, Q.102, L.107, Y.108, F.109 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.67, A:I.70, A:V.76, A:V.79, A:R.83, A:T.100, A:L.107, A:L.107, A:L.107 Hydrogen bonds: A:T.80 Water bridges: A:R.83 pi-Stacking: A:F.109 Halogen bonds: A:K.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rettenmaier, T.J. et al., A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-12-17

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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