SMTL ID : 5lvo.1

Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the PIF-Pocket

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.09 Å

Oligo State

monomer

Ligands

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

ATP.1: 18 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 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.44, A:S.46, A:S.112, A:A.114, A:E.118 Water bridges: A:E.42, A:K.63, A:K.63, A:T.174, A:T.174, A:D.175, A:D.175, A:D.175, A:D.175 Salt bridges: A:K.63

1 x 78W: 2-oxidanylidenepropyl ~{N}-(2-chloranyl-6-fluoranyl-phenyl)carbonyl-~{N}'-(4-chlorophenyl)carbamimidothioate(Non-covalent)

78W.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 9 PLIP interactions: 9 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:Q.102 pi-Stacking: A:F.109 Halogen bonds: A:K.67

1 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

1 x DTD: DITHIANE DIOL(Non-covalent)

DTD.4: 7 residues within 4Å: Chain A: F.194, V.195, G.196, T.197, A.198, V.201, F.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.194 Water bridges: A:G.196

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

CL.5: 4 residues within 4Å: Chain A: I.70, K.75, Y.78, V.79 Ligand excluded by PLIP

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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