5JR2

Crystal structure of the EphA4 LBD in complex with APYd3 peptide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Modifications of a Nanomolar Cyclic Peptide Antagonist for the EphA4 Receptor To Achieve High Plasma Stability.

Olson, E.J.Lechtenberg, B.C.Zhao, C.Rubio de la Torre, E.Lamberto, I.Riedl, S.J.Dawson, P.E.Pasquale, E.B.

(2016) Acs Med.Chem.Lett. 7: 841-846

  • DOI: 10.1021/acsmedchemlett.6b00132

  • PubMed Abstract: 
  • EphA4 is a receptor tyrosine kinase with a critical role in repulsive axon guidance and synaptic function. However, aberrant EphA4 activity can inhibit neural repair after injury and exacerbate neurodegenerative diseases such as amyotrophic lateral s ...

    EphA4 is a receptor tyrosine kinase with a critical role in repulsive axon guidance and synaptic function. However, aberrant EphA4 activity can inhibit neural repair after injury and exacerbate neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and Alzheimer's. We previously identified the cyclic peptide APY-d2 (APYCVYRβASWSC-nh2, containing a disulfide bond) as a potent and selective EphA4 antagonist. However, APY-d2 lacks sufficient plasma stability to be useful for EphA4 inhibition in vivo through peripheral administration. Using structure-activity relationship studies, we show that protecting the peptide N-terminus from proteolytic degradation dramatically increases the persistence of the active peptide in plasma and that a positively charged peptide N-terminus is essential for high EphA4 binding affinity. Among several improved APY-d2 derivatives, the cyclic peptides APY-d3 (βAPYCVYRβASWSC-nh2) and APY-d4 (βAPYCVYRβAEWEC-nh2) combine high stability in plasma and cerebrospinal fluid with slightly enhanced potency. These properties make them valuable research tools and leads toward development of therapeutics for neurological diseases.


    Organizational Affiliation

    Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute , La Jolla, California 92037, United States.,Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States; Pathology Department, University of California, San Diego, La Jolla, California 92093, United States.,Cancer Center, Sanford Burnham Prebys Medical Discovery Institute , La Jolla, California 92037, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ephrin type-A receptor 4
A, B, C, D
179Homo sapiensMutation(s): 1 
Gene Names: EPHA4 (HEK8, SEK, TYRO1)
EC: 2.7.10.1
Find proteins for P54764 (Homo sapiens)
Go to Gene View: EPHA4
Go to UniProtKB:  P54764
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
APYd3 peptide
E, F, G, H
13N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEZ
Query on HEZ

Download SDF File 
Download CCD File 
A, B, C
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
E, F, G, H
NON-POLYMERH2 N

--

BAL
Query on BAL
E, F, G, H
peptide-likeC3 H7 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.137α = 90.00
b = 84.467β = 93.87
c = 127.894γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
Cootmodel building
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS087070
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30CA030199
National Science Foundation (NSF, United States)United StatesDGE-1346837

Revision History 

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-10-05
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.3: 2019-11-27
    Type: Author supporting evidence