5MRD

Human PDK1-PKCiota Kinase Chimera in Complex with Allosteric Compound PS267 Bound to the PIF-Pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An Allosteric Inhibitor Scaffold Targeting the PIF-Pocket of Atypical Protein Kinase C Isoforms.

Arencibia, J.M.Frohner, W.Krupa, M.Pastor-Flores, D.Merker, P.Oellerich, T.Neimanis, S.Schmithals, C.Koberle, V.Su, E.Zeuzem, S.Stark, H.Piiper, A.Odadzic, D.Schulze, J.O.Biondi, R.M.

(2017) ACS Chem. Biol. 12: 564-573

  • DOI: 10.1021/acschembio.6b00827

  • PubMed Abstract: 
  • There is a current and pressing need for improved cancer therapies. The use of small molecule kinase inhibitors and their application in combinatorial regimens represent an approach to personalized targeted cancer therapy. A number of AGC kinases, in ...

    There is a current and pressing need for improved cancer therapies. The use of small molecule kinase inhibitors and their application in combinatorial regimens represent an approach to personalized targeted cancer therapy. A number of AGC kinases, including atypical Protein Kinase C enzymes (PKCs), are validated drug targets for cancer treatment. Most drug development programs for protein kinases focus on the development of drugs that bind at the ATP-binding site. Alternatively, allosteric drugs have great potential for the development of future innovative drugs. However, the rational development of allosteric drugs poses important challenges because the compounds not only must bind to a given site but also must stabilize forms of the protein with a desired effect at a distant site. Here we describe the development of a new class of compounds targeting a regulatory site (PIF-pocket) present in the kinase domain and provide biochemical and crystallographic data showing that these compounds allosterically inhibit the activity of atypical PKCs. PS432, a representative compound, decreased the rate of proliferation of non-small cell lung cancer cells more potently than aurothiomalate, an atypical PKCι inhibitor currently under evaluation in clinical trials, and significantly reduced tumor growth without side effects in a mouse xenograft model. The druglike chemical class provides ample possibilities for the synthesis of derivative compounds, with the potential to allosterically modulate the activity of atypical PKCs and other kinases.


    Organizational Affiliation

    Research Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt , 60590 Frankfurt am Main, Germany.,Department of Hematology/Oncology, Johann Wolfgang Goethe University , Frankfurt am Main, Germany.,Institut für Pharmazeutische Chemie, Johann Wolfgang Goethe Universität , Frankfurt am Main, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg, Germany.,Pharmaceutical and Medicinal Chemistry, Saarland University , Saarbrücken, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-phosphoinositide-dependent protein kinase 1
A
310Homo sapiensMutation(s): 8 
Gene Names: PDPK1 (PDK1)
EC: 2.7.11.1
Find proteins for O15530 (Homo sapiens)
Go to Gene View: PDPK1
Go to UniProtKB:  O15530
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
S26
Query on S26

Download SDF File 
Download CCD File 
A
ethyl (2~{S})-1-(6-chloranyl-1,3-benzothiazol-2-yl)-4-oxidanyl-5-oxidanylidene-2-thiophen-2-yl-2~{H}-pyrrole-3-carboxylate
PS267
C18 H13 Cl N2 O4 S2
PKERYICWLBJVFG-CQSZACIVSA-N
 Ligand Interaction
DTT
Query on DTT

Download SDF File 
Download CCD File 
A
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
S26IC50: 36400 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.140 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 149.110α = 90.00
b = 44.480β = 101.96
c = 47.810γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DFGGermanyBI 1044/2-3
DFGGermanyBI 1044/4-1
DFGGermanyBI 1044/8-1

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Database references
  • Version 1.2: 2017-03-01
    Type: Database references