6CNU

Crystal Structure of JzTX-V


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Discovery of Tarantula Venom-Derived NaV1.7-Inhibitory JzTx-V Peptide 5-Br-Trp24 Analogue AM-6120 with Systemic Block of Histamine-Induced Pruritis.

Wu, B.Murray, J.K.Andrews, K.L.Sham, K.Long, J.Aral, J.Ligutti, J.Amagasu, S.Liu, D.Zou, A.Min, X.Wang, Z.Ilch, C.P.Kornecook, T.J.Lin, M.J.Be, X.Miranda, L.P.Moyer, B.D.Biswas, K.

(2018) J Med Chem 61: 9500-9512

  • DOI: 10.1021/acs.jmedchem.8b00736
  • Primary Citation of Related Structures:  
    6CNU

  • PubMed Abstract: 
  • Inhibitors of the voltage-gated sodium channel Na V 1.7 are being investigated as pain therapeutics due to compelling human genetics. We previously identified Na V 1.7-inhibitory peptides GpTx-1 and JzTx-V from tarantula venom screens ...

    Inhibitors of the voltage-gated sodium channel Na V 1.7 are being investigated as pain therapeutics due to compelling human genetics. We previously identified Na V 1.7-inhibitory peptides GpTx-1 and JzTx-V from tarantula venom screens. Potency and selectivity were modulated through attribute-based positional scans of native residues via chemical synthesis. Herein, we report JzTx-V lead optimization to identify a pharmacodynamically active peptide variant. Molecular docking of peptide ensembles from NMR into a homology model-derived Na V 1.7 structure supported prioritization of key residues clustered on a hydrophobic face of the disulfide-rich folded peptide for derivatization. Replacing Trp24 with 5-Br-Trp24 identified lead peptides with activity in electrophysiology assays in engineered and neuronal cells. 5-Br-Trp24 containing peptide AM-6120 was characterized in X-ray crystallography and pharmacokinetic studies and blocked histamine-induced pruritis in mice after subcutaneous administration, demonstrating systemic Na V 1.7-dependent pharmacodynamics. Our data suggests a need for high target coverage based on plasma exposure for impacting in vivo end points with selectivity-optimized peptidic Na V 1.7 inhibitors.


    Organizational Affiliation

    Therapeutic Discovery, Amgen Research , Amgen Inc. , 1120 Veterans Blvd , South San Francisco , California 94080 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
JzTx-V(D)A31Chilobrachys guangxiensisMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
JzTx-VB31Chilobrachys guangxiensisMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for Q2PAY4 (Chilobrachys guangxiensis)
Explore Q2PAY4 
Go to UniProtKB:  Q2PAY4
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 3 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.16α = 90
b = 37.16β = 90
c = 64.605γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
ACORNphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2018-03-09 
  • Released Date: 2019-03-06 
  • Deposition Author(s): Min, X., Wang, Z.

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 2.0: 2020-03-04
    Type: Coordinate replacement
    Reason: Ligand identity
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary