7O2M | pdb_00007o2m

Crystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus in Complex with Inhibitor MI-2289


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.251 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.183 (Depositor) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 25.6 kDa 
  • Atom Count: 1,574 
  • Modeled Residue Count: 192 
  • Deposited Residue Count: 231 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Genome polyprotein53Zika virusMutation(s): 0 
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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Genome polyprotein178Zika virusMutation(s): 0 
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UZZ
(Subject of Investigation/LOI)

Query on UZZ



Download:Ideal Coordinates CCD File
C [auth B]1-[(3~{S},6~{S},9~{S},19~{R})-3,6-bis(4-azanylbutyl)-2,5,8,12,15,18-hexakis(oxidanylidene)-9-(phenylmethyl)-1,4,7,11,14,17-hexazacyclotricos-19-yl]guanidine
C33 H55 N11 O6
PQMSGIZCMOTKLV-SSUZURRFSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.251 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.183 (Depositor) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.274α = 90
b = 42.274β = 90
c = 216.109γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description