7DOC

Crystal structure of Zika NS2B-NS3 protease with compound 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.209 

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This is version 2.1 of the entry. See complete history


Literature

2-Cyanoisonicotinamide Conjugation: A Facile Approach to Generate Potent Peptide Inhibitors of the Zika Virus Protease.

Patil, N.A.Quek, J.P.Schroeder, B.Morewood, R.Rademann, J.Luo, D.Nitsche, C.

(2021) ACS Med Chem Lett 12: 732-737

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00657
  • Primary Citation of Related Structures:  
    7DOC

  • PubMed Abstract: 

    The rapid generation and modification of macrocyclic peptides in medicinal chemistry is an ever-growing area that can present various synthetic challenges. The reaction between N-terminal cysteine and 2-cyanoisonicotinamide is a new biocompatible click reaction that allows rapid access to macrocyclic peptides. Importantly, 2-cyanoisonicotinamide can be attached to different linkers directly during solid-phase peptide synthesis. The synthesis involves only commercially available precursors, allowing for a fully automated process. We demonstrate the approach for four cyclic peptide ligands of the Zika virus protease NS2B-NS3. Although all peptides display the substrate recognition motif, the activity strongly depends on the linker length, with the shortest cyclization linker corresponding to highest activity ( K i = 0.64 μM). The most active cyclic peptide displays affinity 78 times higher than that of its linear analogue. We solved a crystal structure of the proteolytically cleaved ligand and synthesized it by applying the presented chemistry to peptide ligation.


  • Organizational Affiliation

    Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Core protein
A, G
39Zika virusMutation(s): 0 
Gene Names: GP1A2G93_72127gpGP1
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for Q32ZE1 (Zika virus)
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UniProt GroupQ32ZE1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Core protein153Zika virusMutation(s): 0 
Gene Names: GP1A2G93_63394gpGP1
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
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UniProt GroupQ32ZE1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein38Zika 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
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UniProt GroupQ32ZE1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Core protein152Zika virusMutation(s): 0 
Gene Names: GP1A2G93_63394gpGP1
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
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UniProt GroupQ32ZE1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Serine protease subunit NS2B39Zika virusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Core protein158Zika virusMutation(s): 0 
Gene Names: GP1A2G93_63394gpGP1
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for Q32ZE1 (Zika virus)
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UniProt GroupQ32ZE1
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein153Zika virusMutation(s): 0 
UniProt
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Explore Q32ZE1 
Go to UniProtKB:  Q32ZE1
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE5synthetic constructMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.154α = 90
b = 59.614β = 90
c = 215.073γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2021-04-14 
  • Deposition Author(s): Quek, J.P.

Funding OrganizationLocationGrant Number
Other governmentSingaporeStart up grant
Other governmentSingaporeCBRG15May045
Other governmentSingaporeNRF2016NRF-CRP001-063

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2023-11-29
    Changes: Refinement description