6FNC

Mono- and bivalent 14-3-3 inhibitors for characterizing supramolecular lysine-PEG interactions in proteins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mono- and Bivalent 14-3-3 Inhibitors for Characterizing Supramolecular "Lysine Wrapping" of Oligoethylene Glycol (OEG) Moieties in Proteins.

Yilmaz, E.Bier, D.Guillory, X.Briels, J.Ruiz-Blanco, Y.B.Sanchez-Garcia, E.Ottmann, C.Kaiser, M.

(2018) Chemistry 24: 13807-13814

  • DOI: 10.1002/chem.201801074
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Previous studies have indicated the presence of defined interactions between oligo or poly(ethylene glycol) (OEG or PEG) and lysine residues. In these interactions, the OEG or PEG residues "wrap around" the lysine amino group, thereby enabling comple ...

    Previous studies have indicated the presence of defined interactions between oligo or poly(ethylene glycol) (OEG or PEG) and lysine residues. In these interactions, the OEG or PEG residues "wrap around" the lysine amino group, thereby enabling complexation of the amino group by the ether oxygen residues. The resulting biochemical binding affinity and thus biological relevance of this supramolecular interaction however remains unclear so far. Here, we report that OEG-containing phosphophenol ether inhibitors of 14-3-3 proteins also display such a "lysine-wrapping" binding mode. For better investigating the biochemical relevance of this binding mode, we made use of the dimeric nature of 14-3-3 proteins and designed as well as synthesized a set of bivalent 14-3-3 inhibitors for biochemical and X-ray crystallography-based structural studies. We found that all synthesized derivatives adapted the "lysine-wrapping" binding mode in the crystal structures; in solution, a different binding mode is however observed, most probably as the "lysine-wrapping" binding mode turned out to be a rather weak interaction. Accordingly, our studies demonstrate that structural studies of OEG-lysine interactions are difficult to interpret and their presence in structural studies may not automatically be correlated with a relevant interaction also in solution but requires further biochemical studies.


    Organizational Affiliation

    Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Braunschweig, Germany.,Chemical Biology, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Department of Chemistry, Université de Montréal, Montréal, QC, H3C 3J7, Canada.,Center of Pharmaceutical Engeneering (PVZ), Technische Universität Braunschweig, Braunschweig, Germany.,Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA. sfanning@uchicago.edu.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands.,Computational Biochemistry, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.,Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, China.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA.,Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,College of Life Sciences, Peking University, Beijing 100871, China.,Université de Lorraine, LERMAB, Nancy, France.,Olema Pharmaceuticals, San Francisco, CA, 94107, USA.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada.,Université de Lorraine, CNRS, CRM2, Nancy, France. claude.didierjean@univ-lorraine.fr.,Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom.,College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China.,Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,DISFARM, Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica, Università degli Studi, Milano, Italy.,Université de Lorraine, INRA, IAM, Nancy, France.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,Max-Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.,Institute of Biochemistry, University of Cologne, 50674 Koeln, Germany.,Department of Medical Sciences, Rheumatology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Université de Lorraine, CNRS, CRM2, Nancy, France.,Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA.,Institute for Pharmaceutical Chemistry, Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.,Université de Lorraine, INRA, IAM, Nancy, France. eric.gelhaye@univ-lorraine.fr.,Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA.,ManRos Therapeutics, Hôtel de Recherche, Centre de Perharidy, Roscoff, France.,Olema Pharmaceuticals, San Francisco, CA, 94107, USA. leslie@olemapharma.com.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.,Pfizer Worldwide Research & Development , 610 Main Street, Cambridge, Massachusetts 02139, United States.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada. john.pascal@umontreal.ca.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA. blackbe@pennmedicine.upenn.edu.,Tetramer Core, BRI at Virginia Mason, Seattle, WA, USA.,Translational Research Program, BRI at Virginia Mason, Seattle, WA, USA.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden. Electronic address: Vivianne.malmstrom@ki.se.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
14-3-3 protein zeta/delta
A, B
230Homo sapiensMutation(s): 0 
Gene Names: YWHAZ
Find proteins for P63104 (Homo sapiens)
Go to Gene View: YWHAZ
Go to UniProtKB:  P63104
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BEZ
Query on BEZ

Download SDF File 
Download CCD File 
A, B
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
 Ligand Interaction
DWK
Query on DWK

Download SDF File 
Download CCD File 
A, B
[2-[2-oxidanylidene-2-[[3-[3-[2-[2-[3-[[4-[2-(2-phosphonophenoxy)ethanoylamino]phenyl]carbonylamino]propoxy]ethoxy]ethoxy]propylcarbamoyl]phenyl]amino]ethoxy]phenyl]phosphonic acid
C40 H48 N4 O15 P2
UMUYNCNMFPOMAG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.999α = 90.00
b = 102.992β = 90.00
c = 113.875γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-02-02 
  • Released Date: 2018-07-04 
  • Deposition Author(s): Bier, D., Ottann, C.

Funding OrganizationLocationGrant Number
German Research FoundationGermanyCRC1093 (Supramolecular Chemistry on Proteins)

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-10-03
    Type: Data collection, Database references
  • Version 1.2: 2018-12-19
    Type: Data collection, Derived calculations