4I7B

Siah1 bound to synthetic peptide (ACE)KLRPV(ABA)MVRPTVR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based design of covalent siah inhibitors.

Stebbins, J.L.Santelli, E.Feng, Y.De, S.K.Purves, A.Motamedchaboki, K.Wu, B.Ronai, Z.A.Liddington, R.C.Pellecchia, M.

(2013) Chem.Biol. 20: 973-982

  • DOI: 10.1016/j.chembiol.2013.06.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The E3 ubiquitin ligase Siah regulates key cellular events that are central to cancer development and progression. A promising route to Siah inhibition is disrupting its interactions with adaptor proteins. However, typical of protein-protein interact ...

    The E3 ubiquitin ligase Siah regulates key cellular events that are central to cancer development and progression. A promising route to Siah inhibition is disrupting its interactions with adaptor proteins. However, typical of protein-protein interactions, traditional unbiased approaches to ligand discovery did not produce viable hits against this target, despite considerable effort and a multitude of approaches. Ultimately, a rational structure-based design strategy was successful for the identification of Siah inhibitors in which peptide binding drives specific covalent bond formation with the target. X-ray crystallography, mass spectrometry, and functional data demonstrate that these peptide mimetics are efficient covalent inhibitors of Siah and antagonize Siah-dependent regulation of Erk and Hif signaling in the cell. The proposed strategy may result useful as a general approach to the design of peptide-based inhibitors of other protein-protein interactions.


    Organizational Affiliation

    Signal Transduction Program and Cell Death Program, Cancer Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase SIAH1
A, C
196Homo sapiensMutation(s): 0 
Gene Names: SIAH1 (HUMSIAH)
EC: 2.3.2.27
Find proteins for Q8IUQ4 (Homo sapiens)
Go to Gene View: SIAH1
Go to UniProtKB:  Q8IUQ4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein phyllopod
B, D
14Drosophila melanogasterMutation(s): 0 
Gene Names: phyl
Find proteins for Q27934 (Drosophila melanogaster)
Go to UniProtKB:  Q27934
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000939
Query on PRD_000939
B,Dmodified protein phyllopod peptide BI-117E1Oligopeptide / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.745α = 90.00
b = 87.913β = 100.59
c = 59.884γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PHASERphasing
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-09-11
    Type: Database references