4I7C

Siah1 mutant bound to synthetic peptide (ACE)KLRPV(23P)MVRPWVR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

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:  
    4I7B, 4I7C, 4I7D

  • 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 interactions, traditional unbiased approaches to ligand discovery did not produce viable hits against this target, despite considerable effort and a multitude of approaches ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase SIAH1A, C196Homo sapiensMutation(s): 1 
Gene Names: SIAH1HUMSIAH
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IUQ4 (Homo sapiens)
Explore Q8IUQ4 
Go to UniProtKB:  Q8IUQ4
PHAROS:  Q8IUQ4
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein phyllopodB, D14Drosophila melanogasterMutation(s): 2 
Gene Names: phylCG10108
UniProt
Find proteins for Q27934 (Drosophila melanogaster)
Explore Q27934 
Go to UniProtKB:  Q27934
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
23P
Query on 23P
B, DL-PEPTIDE LINKINGC6 H12 N2 O3ALA
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.23α = 90
b = 164.23β = 90
c = 164.23γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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