7VLH

Crystal structure of Zika NS2B-NS3 protease with compound MI2219

  • Classification: VIRAL PROTEIN
  • Organism(s): Zika virus
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2021-10-02 Released: 2022-08-10 
  • Deposition Author(s): Quek, J.P.
  • Funding Organization(s): National Research Foundation (NRF, Singapore)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.239 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-Based Optimization and Characterization of Macrocyclic Zika Virus NS2B-NS3 Protease Inhibitors.

Huber, S.Braun, N.J.Schmacke, L.C.Quek, J.P.Murra, R.Bender, D.Hildt, E.Luo, D.Heine, A.Steinmetzer, T.

(2022) J Med Chem 65: 6555-6572

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01860
  • Primary Citation of Related Structures:  
    7O2M, 7O55, 7OBV, 7OC2, 7PFQ, 7PFY, 7PFZ, 7PG1, 7PGC, 7VLG, 7VLH, 7VLI

  • PubMed Abstract: 

    Zika virus (ZIKV) is a human pathogenic arbovirus. So far, neither a specific treatment nor a vaccination against ZIKV infections has been approved. Starting from our previously described lead structure, a series of 29 new macrocyclic inhibitors of the Zika virus protease containing different linker motifs have been synthesized. By selecting hydrophobic d-amino acids as part of the linker, numerous inhibitors with K i values < 5 nM were obtained. For 12 inhibitors, crystal structures in complex with the ZIKV protease up to 1.30 Å resolution were determined, which contribute to the understanding of the observed structure-activity relationship (SAR). In immunofluorescence assays, an antiviral effect was observed for compound 26 containing a d-homocyclohexylalanine residue in its linker segment. Due to its excellent selectivity profile and low cytotoxicity, this inhibitor scaffold could be a suitable starting point for the development of peptidic drugs against the Zika virus and related flaviviruses.


  • Organizational Affiliation

    Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine protease subunit NS2B53Zika virusMutation(s): 0 
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.1.1.56 (PDB Primary Data), 2.1.1.57 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for Q32ZE1 (Zika virus)
Explore Q32ZE1 
Go to UniProtKB:  Q32ZE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ32ZE1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NS3 protease178Zika virusMutation(s): 0 
Gene Names: GP1A2G93_63394gpGP1
UniProt
Find proteins for Q32ZE1 (Zika virus)
Explore Q32ZE1 
Go to UniProtKB:  Q32ZE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ32ZE1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7Q3 (Subject of Investigation/LOI)
Query on 7Q3

Download Ideal Coordinates CCD File 
C [auth B]1-[(3~{S},6~{R},18~{R})-3,6-bis(4-azanylbutyl)-2,5,8,11,14,17-hexakis(oxidanylidene)-1,4,7,10,13,16-hexazacyclodocos-18-yl]guanidine
C25 H47 N11 O6
WWPJZTJFBPQVSG-RCCFBDPRSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.239 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.992α = 90
b = 40.992β = 90
c = 214.435γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2022-08-10 
  • Deposition Author(s): Quek, J.P.

Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Singapore)SingaporeNRF2016NRF-CRP001-063

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary