6KPQ

Crystal structure of Zika NS2B-NS3 protease with compound 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-Based Macrocyclization of Substrate Analogue NS2B-NS3 Protease Inhibitors of Zika, West Nile and Dengue viruses.

Braun, N.J.Quek, J.P.Huber, S.Kouretova, J.Rogge, D.Lang-Henkel, H.Cheong, E.Z.K.Chew, B.L.A.Heine, A.Luo, D.Steinmetzer, T.

(2020) ChemMedChem 15: 1439-1452

  • DOI: 10.1002/cmdc.202000237
  • Primary Citation of Related Structures:  
    6KK3, 6KK2, 6KK5, 6KK4, 6KK6, 6KPQ, 6Y3B

  • PubMed Abstract: 
  • A series of cyclic active-site-directed inhibitors of the NS2B-NS3 proteases from Zika (ZIKV), West Nile (WNV), and dengue-4 (DENV4) viruses has been designed. The most potent compounds contain a reversely incorporated d-lysine residue in the P1 position ...

    A series of cyclic active-site-directed inhibitors of the NS2B-NS3 proteases from Zika (ZIKV), West Nile (WNV), and dengue-4 (DENV4) viruses has been designed. The most potent compounds contain a reversely incorporated d-lysine residue in the P1 position. Its side chain is connected to the P2 backbone, its α-amino group is converted into a guanidine to interact with the conserved Asp129 side chain in the S1 pocket, and its C terminus is connected to the P3 residue via different linker segments. The most potent compounds inhibit the ZIKV protease with K i values <5 nM. Crystal structures of seven ZIKV protease inhibitor complexes were determined to support the inhibitor design. All the cyclic compounds possess high selectivity against trypsin-like serine proteases and furin-like proprotein convertases. Both WNV and DENV4 proteases are inhibited less efficiently. Nonetheless, similar structure-activity relationships were observed for these enzymes, thus suggesting their potential application as pan-flaviviral protease inhibitors.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine protease subunit NS2BA53Zika 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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NS3 proteaseB178Zika virusMutation(s): 0 
Gene Names: GP1A2G93_63394gpGP1
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q32ZE1 (Zika virus)
Explore Q32ZE1 
Go to UniProtKB:  Q32ZE1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DT0
Query on DT0

Download Ideal Coordinates CCD File 
C [auth B]1-[(10~{R},17~{S},20~{S})-17,20-bis(4-azanylbutyl)-4,9,16,19,22-pentakis(oxidanylidene)-3,8,15,18,21-pentazabicyclo[22.3.1]octacosa-1(27),24(28),25-trien-10-yl]guanidine
C32 H54 N10 O5
YJXCERDQNKQGCK-NXCFDTQHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.218 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.586α = 90
b = 42.586β = 90
c = 214.18γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-08-15 
  • Released Date: 2020-06-17 
  • 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: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references