6GHP

14-3-3sigma in complex with a TASK3 peptide stabilized by semi-synthetic natural product FC-NAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Rationally Designed Semisynthetic Natural Product Analogues for Stabilization of 14-3-3 Protein-Protein Interactions.

Andrei, S.A.de Vink, P.Sijbesma, E.Han, L.Brunsveld, L.Kato, N.Ottmann, C.Higuchi, Y.

(2018) Angew. Chem. Int. Ed. Engl. 57: 13470-13474

  • DOI: 10.1002/anie.201806584

  • PubMed Abstract: 
  • The natural product family of fusicoccanes are stabilizers of 14-3-3 mediated protein-protein interactions (PPIs), some of which possess antitumor activity. In this study, the first use of molecular dynamics (MD) to rationally design PPI stabilizers ...

    The natural product family of fusicoccanes are stabilizers of 14-3-3 mediated protein-protein interactions (PPIs), some of which possess antitumor activity. In this study, the first use of molecular dynamics (MD) to rationally design PPI stabilizers with increased potency is presented. Synthesis of a focused library, with subsequent characterization by fluorescence polarization, mutational studies, and X-ray crystallography confirmed the power of the MD-based design approach, revealing the potential for an additional hydrogen bond with the 14-3-3 protein to lead to significantly increased potency. Additionally, these compounds exert their action in a cellular environment with increased potency. The newly found polar interaction could provide an anchoring point for new small-molecule PPI stabilizers. These results facilitate the development of fusicoccanes towards drugs or tool compounds, as well as allowing the study of the fundamental principles behind PPI stabilization.


    Organizational Affiliation

    Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands.,The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan.,Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
14-3-3 protein sigma
A
236Homo sapiensMutation(s): 0 
Gene Names: SFN (HME1)
Find proteins for P31947 (Homo sapiens)
Go to Gene View: SFN
Go to UniProtKB:  P31947
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Potassium channel subfamily K member 9
P
7Homo sapiensMutation(s): 0 
Gene Names: KCNK9 (TASK3)
Find proteins for Q9NPC2 (Homo sapiens)
Go to Gene View: KCNK9
Go to UniProtKB:  Q9NPC2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EZ5
Query on EZ5

Download SDF File 
Download CCD File 
A
~{N}-[(2~{S})-2-[(1~{E},3~{R},4~{S},8~{R},9~{R},10~{R},11~{S},14~{S})-14-(methoxymethyl)-3,10-dimethyl-8-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(2-methylbut-3-en-2-yloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,9-bis(oxidanyl)-6-tricyclo[9.3.0.0^{3,7}]tetradeca-1,6-dienyl]propyl]ethanamide
C34 H55 N O10
HCYVTSJOORQWMP-AHQPFIERSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
SEP
Query on SEP
P
L-PEPTIDE LINKINGC3 H8 N O6 PSER
ACE
Query on ACE
P
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.181 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 82.453α = 90.00
b = 111.473β = 90.00
c = 63.675γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific ResearchNetherlandsECHO -STIP 717.014.001
Netherlands Organisation for Scientific ResearchNetherlandsGravity program 024.001.035
Japan Society for the Promotion of ScienceJapanKAKENHI Grant JP 16K21138
Japan Agency for Medical Research and Development (AMED)JapanPlatform Project for Supporting Drug Discovery and Life Science Research

Revision History 

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references, Structure summary