SMTL ID : 5ack.1

Human PDK1 Kinase Domain in Complex with Allosteric Compound 7 Bound to the PIF-Pocket

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

monomer

Ligands

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

ATP.1: 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, L.164, T.174 Ligands: NA.5, NA.7 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.43, A:S.44, A:S.46, A:S.46, A:S.112, A:A.114, A:E.118 Water bridges: A:F.45, A:S.46, A:Y.78 Salt bridges: A:K.63

1 x SVQ: 1-(4-CHLOROPHENETHYL)-2-(2-CHLOROPHENYL)-6-OXOPIPERIDINE-3-CARBOXYLIC ACID(Non-covalent)

SVQ.2: 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:R.83, A:L.107, A:F.109 Hydrogen bonds: A:Q.102 Halogen bonds: A:K.67, A:V.79

1 x DTD: DITHIANE DIOL(Non-covalent)

DTD.3: 8 residues within 4Å: Chain A: F.194, V.195, G.196, T.197, A.198, V.201, E.239, F.243 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.196 Water bridges: A:G.196, A:E.239

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

DMS.4: 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

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

NA.5: 5 residues within 4Å: Chain A: K.63, Y.78, D.175 Ligands: ATP.1, NA.7 No protein-ligand interaction detected (PLIP) NA.6: 4 residues within 4Å: Chain A: D.157, K.159, G.196, T.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.159, A:G.196 Water bridges: A:G.196 NA.7: 4 residues within 4Å: Chain A: N.162, D.175 Ligands: ATP.1, NA.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.162, A:N.162, A:D.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kroon, E. et al., Discovery of a Potent Allosteric Kinase Modulator by Combining Computational and Synthetic Methods. Angew.Chem.Int.Ed.Engl. (2015)

Release Date

2015-10-21

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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