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 6CNU | pdb_00006cnu

Crystal Structure of JzTX-V


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 
    0.209 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6CNU

This is version 2.1 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: https://doi.org/10.1021/acs.jmedchem.8b00736
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 7.85 kDa 
  • Atom Count: 611 
  • Modeled Residue Count: 62 
  • Deposited Residue Count: 62 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
JzTx-V(D)31Chilobrachys guangxiensisMutation(s): 0 
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
JzTx-V31Chilobrachys guangxiensisMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for Q2PAY4 (Chilobrachys guangxiensis)
Explore Q2PAY4 
Go to UniProtKB:  Q2PAY4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2PAY4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  16 Unique
IDChains TypeFormula2D DiagramParent
DAL
Query on DAL
A
D-PEPTIDE LINKINGC3 H7 N O2

--

DAR
Query on DAR
A
D-PEPTIDE LINKINGC6 H15 N4 O2

--

DAS
Query on DAS
A
D-PEPTIDE LINKINGC4 H7 N O4

--

DCY
Query on DCY
A
D-PEPTIDE LINKINGC3 H7 N O2 S

--

DGL
Query on DGL
A
D-PEPTIDE LINKINGC5 H9 N O4

--

DGN
Query on DGN
A
D-PEPTIDE LINKINGC5 H10 N2 O3

--

DIL
Query on DIL
A
D-PEPTIDE LINKINGC6 H13 N O2

--

DLE
Query on DLE
A
D-PEPTIDE LINKINGC6 H13 N O2

--

DLY
Query on DLY
A
D-PEPTIDE LINKINGC6 H14 N2 O2

--

DSN
Query on DSN
A
D-PEPTIDE LINKINGC3 H7 N O3

--

DTH
Query on DTH
A
D-PEPTIDE LINKINGC4 H9 N O3

--

DTR
Query on DTR
A
D-PEPTIDE LINKINGC11 H12 N2 O2

--

F9D
Query on F9D
A
D-PEPTIDE LINKINGC5 H7 N O2

--

MED
Query on MED
A
D-PEPTIDE LINKINGC5 H11 N O2 S

--

LPH
Query on LPH
B
L-PEPTIDE LINKINGC5 H7 N O2

--

MSE
Query on MSE
B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free:  0.209 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
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

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
  • Version 2.1: 2025-04-02
    Changes: Data collection, Database references, Derived calculations, Structure summary