9CY8

Constrained b-hairpins targeting the EphA4 ligand binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.257 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Constrained beta-Hairpins Targeting the EphA4 Ligand Binding Domain.

Prentiss, A.M.Baggio, C.Pagett, J.Kulinich, A.O.Ethell, I.M.Muzzarelli, K.Assar, Z.Pellecchia, M.

(2024) J Med Chem 67: 22245-22253

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02286
  • Primary Citation of Related Structures:  
    9CY8

  • PubMed Abstract: 

    The activity of the receptor tyrosine kinase EphA4 has been implicated in several pathologies including oncology (gastric and pancreatic cancers) and neurodegenerative diseases (amyotrophic lateral sclerosis and Alzheimer's disease). However, advances in validating EphA4 as a possible drug target have been limited by the lack of suitable pharmacological inhibitors. Recently, we reported on the design of potent EphA4 agonistic agents targeting its ligand binding domain (LBD). Based on previous studies with a phage display cyclic peptide inhibitor, we designed a β-hairpin mimetic with high affinity for EphA4-LBD. These agents hold great promise for further validation and development of EphA4-based therapeutics. Moreover, our studies introduce a possible strategy for the design of constrained β-hairpin peptides.


  • Organizational Affiliation

    Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ephrin type-A receptor 4185Homo sapiensMutation(s): 0 
Gene Names: EPHA4HEK8SEKTYRO1
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P54764 (Homo sapiens)
Explore P54764 
Go to UniProtKB:  P54764
PHAROS:  P54764
GTEx:  ENSG00000116106 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54764
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Constrained b-hairpin13synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
NLE
Query on NLE
B
L-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.257 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.059α = 90
b = 128.053β = 90
c = 34.907γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-01-01
    Changes: Database references, Source and taxonomy