5EK0

Human Nav1.7-VSD4-NavAb in complex with GX-936.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.53 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of Nav1.7 inhibition by an isoform-selective small-molecule antagonist.

Ahuja, S.Mukund, S.Deng, L.Khakh, K.Chang, E.Ho, H.Shriver, S.Young, C.Lin, S.Johnson, J.P.Wu, P.Li, J.Coons, M.Tam, C.Brillantes, B.Sampang, H.Mortara, K.Bowman, K.K.Clark, K.R.Estevez, A.Xie, Z.Verschoof, H.Grimwood, M.Dehnhardt, C.Andrez, J.C.Focken, T.Sutherlin, D.P.Safina, B.S.Starovasnik, M.A.Ortwine, D.F.Franke, Y.Cohen, C.J.Hackos, D.H.Koth, C.M.Payandeh, J.

(2015) Science 350: aac5464-aac5464

  • DOI: 10.1126/science.aac5464

  • PubMed Abstract: 
  • Voltage-gated sodium (Nav) channels propagate action potentials in excitable cells. Accordingly, Nav channels are therapeutic targets for many cardiovascular and neurological disorders. Selective inhibitors have been challenging to design because the ...

    Voltage-gated sodium (Nav) channels propagate action potentials in excitable cells. Accordingly, Nav channels are therapeutic targets for many cardiovascular and neurological disorders. Selective inhibitors have been challenging to design because the nine mammalian Nav channel isoforms share high sequence identity and remain recalcitrant to high-resolution structural studies. Targeting the human Nav1.7 channel involved in pain perception, we present a protein-engineering strategy that has allowed us to determine crystal structures of a novel receptor site in complex with isoform-selective antagonists. GX-936 and related inhibitors bind to the activated state of voltage-sensor domain IV (VSD4), where their anionic aryl sulfonamide warhead engages the fourth arginine gating charge on the S4 helix. By opposing VSD4 deactivation, these compounds inhibit Nav1.7 through a voltage-sensor trapping mechanism, likely by stabilizing inactivated states of the channel. Residues from the S2 and S3 helices are key determinants of isoform selectivity, and bound phospholipids implicate the membrane as a modulator of channel function and pharmacology. Our results help to elucidate the molecular basis of voltage sensing and establish structural blueprints to design selective Nav channel antagonists.


    Organizational Affiliation

    Department of Structural Biology, Genentech Inc., South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha
A, B, C, D
296Homo sapiensArcobacter butzleri (strain RM4018)
This entity is chimeric
Mutation(s): 0 
Gene Names: SCN9A (NENA),
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Potassium, Sodium, & Proton Ion-Selective
Protein: 
NaV1.7 VSD4 voltage dependent sodium channel
Find proteins for Q15858 (Homo sapiens)
Go to Gene View: SCN9A
Go to UniProtKB:  Q15858
Find proteins for A8EVM5 (Arcobacter butzleri (strain RM4018))
Go to UniProtKB:  A8EVM5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5P2
Query on 5P2

Download SDF File 
Download CCD File 
A, B, C, D
3-cyano-4-[2-[2-(1-ethylazetidin-3-yl)pyrazol-3-yl]-4-(trifluoromethyl)phenoxy]-~{N}-(1,2,4-thiadiazol-5-yl)benzenesulfonamide
GX-936
C24 H20 F3 N7 O3 S2
UCAVSLIXTXZSRD-UHFFFAOYSA-N
 Ligand Interaction
PX4
Query on PX4

Download SDF File 
Download CCD File 
A, B, C, D
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.53 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.243 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 169.420α = 90.00
b = 188.830β = 90.00
c = 171.130γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
Aimlessdata scaling
iMOSFLMdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2015-12-30
    Type: Database references