SMTL ID : 5lvl.1

Human PDK1 Kinase Domain in Complex with Compound PS653 Bound to the ATP-Binding Site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x 537: 2,6-DIHYDROANTHRA/1,9-CD/PYRAZOL-6-ONE(Non-covalent)

537.1: 12 residues within 4Å: Chain A: L.40, G.41, V.48, A.61, V.95, L.111, S.112, Y.113, A.114, G.117, L.164, T.174 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.40, A:V.48, A:L.111, A:L.164 Hydrogen bonds: A:S.112, A:A.114

1 x DTD: DITHIANE DIOL(Non-covalent)

DTD.2: 9 residues within 4Å: Chain A: F.194, V.195, G.196, T.197, A.198, V.201, L.206, E.239, F.243 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.194 Water bridges: A:G.196, A:G.196

3 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: 6 residues within 4Å: Chain A: P.31, F.36, V.49, I.64, K.106, Y.108 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.36 DMS.5: 6 residues within 4Å: Chain A: L.249, Y.251, D.252, F.253, R.262, E.266 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.262 pi-Cation interactions: A:Y.251

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulze, J.O. et al., Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase. Cell Chem Biol (2016)

Release Date

2016-10-19

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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