SMTL ID : 4aw0.1

Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the PIF-Pocket

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

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

ATP.1: 20 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, L.164, T.174, D.175 Ligands: MG.4, MG.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.44, A:S.44, A:S.44, A:S.46, A:S.112, A:A.114, A:E.118 Water bridges: A:E.42, A:E.42, A:F.45, A:E.118, A:T.174, A:T.174 Salt bridges: A:K.63

1 x MJF: [(1R)-3-(4-chlorophenyl)-3-oxo-1-phenylpropyl]propanedioic acid(Non-covalent)

MJF.2: 14 residues within 4Å: Chain A: K.28, 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 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.100, A:L.107, A:L.107, A:L.107 Hydrogen bonds: A:T.100, A:Q.102 Salt bridges: A:K.28, A:K.28, A:R.83, A:R.83 pi-Stacking: A:F.109

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 8 residues within 4Å: Chain A: H.91, P.92, F.93, W.299, E.300, N.301, L.302, H.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.303, A:H.303

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: K.63, D.175 Ligands: ATP.1, MG.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.175 MG.5: 4 residues within 4Å: Chain A: N.162, D.175 Ligands: ATP.1, MG.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.175

1 x DTD: DITHIANE DIOL(Non-covalent)

DTD.6: 8 residues within 4Å: Chain A: F.194, V.195, G.196, T.197, A.198, V.201, E.239, F.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.239 Water bridges: A:G.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Busschots, K. et al., Substrate-Selective Inhibition of Protein Kinase Pdk1 by Small Compounds that Bind to the Pif-Pocket Allosteric Docking Site. Chem.Biol. (2012)

Release Date

2012-10-03

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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