SMTL ID : 4rqk.1

Crystal structure of PDK1 in complex with ATP and the PIF-pocket ligand RS1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: H.91, P.92, F.93, S.143, W.299, E.300, N.301, L.302, H.303 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.91, A:E.300, A:L.302, A:H.303 Water bridges: A:S.143 GOL.2: 3 residues within 4Å: Chain A: F.34, K.35, F.36 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.36, A:F.36 Water bridges: A:F.34

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

ATP.3: 19 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, D.175 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.43, A:S.44, A:S.44, A:S.44, A:S.46, A:S.46, A:S.112, A:A.114, A:E.118, A:E.118, A:D.175 Water bridges: A:K.159, A:T.174 Salt bridges: A:K.63

1 x R1S: N-(6-chloro-1,3-benzothiazol-2-yl)-1-benzothiophene-3-sulfonamide(Non-covalent)

R1S.4: 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.67, A:I.70, A:L.107, A:L.107, A:L.107 Hydrogen bonds: A:R.83 Halogen bonds: A:K.67

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 10 residues within 4Å: Chain A: L.120, I.123, R.124, G.127, Q.199, Y.200, Q.226, G.230, L.231, P.232 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.124, A:Q.226 Water bridges: A:R.124, A:E.161, A:E.161 Salt bridges: A:R.124

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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