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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/acs.jmedchem.8b00736

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

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
JzTx-V(D)
A
30N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
JzTx-V
B
30Chilobrachys guangxiensisMutation(s): 0 
Find proteins for Q2PAY4 (Chilobrachys guangxiensis)
Go to UniProtKB:  Q2PAY4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download SDF File 
Download CCD File 
A, B
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
NH4
Query on NH4

Download SDF File 
Download CCD File 
A, B
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  16 Unique
IDChainsTypeFormula2D DiagramParent
F9D
Query on F9D
A
D-peptide linkingC5 H7 N O2

--

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

--

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

--

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

--

LPH
Query on LPH
B
L-peptide linkingC5 H7 N O2

--

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

--

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

--

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

--

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

--

DAL
Query on DAL
A
D-PEPTIDE LINKINGC3 H7 N O2

--

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

--

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

--

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

--

MSE
Query on MSE
B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
DTR
Query on DTR
A
D-PEPTIDE LINKINGC11 H12 N2 O2

--

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

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.190 
  • Space Group: P 3 1 2
Unit Cell:
Length (Å)Angle (°)
a = 37.160α = 90.00
b = 37.160β = 90.00
c = 64.605γ = 120.00
Software Package:
Software NamePurpose
ACORNphasing
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-07-03
    Type: Data collection, Database references, Derived calculations, Source and taxonomy