9CY8 | pdb_00009cy8

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
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9CY8

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 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.

Macromolecule Content 

  • Total Structure Weight: 22.81 kDa 
  • Atom Count: 1,557 
  • Modeled Residue Count: 186 
  • Deposited Residue Count: 198 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Constrained b-hairpin13synthetic constructMutation(s): 0 

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
BAL
Query on BAL
B
PEPTIDE-LIKEC3 H7 N O2

--

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

View Full Validation Report



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