SMTL ID : 4aw1.1

Human PDK1 Kinase Domain in Complex with Allosteric Compound PS210 Bound to the PIF-Pocket

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

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

ATP.1: 23 residues within 4Å: Chain A: L.40, G.41, E.42, G.43, S.44, F.45, S.46, V.48, A.61, K.63, V.95, L.111, S.112, Y.113, A.114, E.118, E.161, N.162, L.164, T.174, D.175 Ligands: MN.5, NA.6 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.44, A:S.46, A:S.112, A:A.114, A:E.118 Water bridges: A:G.117, A:E.118, A:K.159, A:E.161, A:E.161, A:T.174, A:D.175 Salt bridges: A:K.63, A:K.63

1 x 21O: {(1R)-3-oxo-1-phenyl-3-[4-(trifluoromethyl)phenyl]propyl}propanedioic acid(Non-covalent)

21O.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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.76, A:V.79, A:T.100, A:L.107, A:L.107, A:L.107 Hydrogen bonds: A:T.100, A:Q.102 Water bridges: A:Q.102 Salt bridges: A:K.28, A:K.28, A:R.83, A:R.83 pi-Stacking: A:F.109

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

DMS.3: 9 residues within 4Å: Chain A: H.91, P.92, F.93, S.143, 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 DMS.4: 5 residues within 4Å: Chain A: I.123, R.124, G.127, G.230, L.231 No protein-ligand interaction detected (PLIP)

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.5: 5 residues within 4Å: Chain A: K.63, D.175, T.178 Ligands: ATP.1, NA.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.175, A:D.175

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 4 residues within 4Å: Chain A: N.162, D.175 Ligands: ATP.1, MN.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.162 Water bridges: A:D.157, A:E.161, A:N.162 NA.7: 4 residues within 4Å: Chain A: H.91, S.143, E.146, Y.147 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.146, A:Y.147 Water bridges: A:H.91, A:K.289

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 3 residues within 4Å: Chain A: I.64, K.106, Y.108 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: G.37, L.50, A.51, R.52 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: Q.199, A.236, I.242 Ligand excluded by PLIP

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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