6KK3

Crystal structure of Zika NS2B-NS3 protease with compound 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.189 

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:  
    6Y3B, 6KK3, 6KK2, 6KK5, 6KK4, 6KK6, 6KPQ

  • 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 was designed. The most potent compounds contain a reversely incorporated d-lysine residue in P1 position, w ...

    A series of cyclic active-site directed inhibitors of the NS2B-NS3 proteases from Zika- (ZIKV), West Nile- (WNV), and Dengue-4 (DENV4) viruses was designed. The most potent compounds contain a reversely incorporated d-lysine residue in P1 position, where its side chain is connected to the P2 backbone, its a-amino group is converted into a guanidine for interaction with the conserved Asp129 side chain in the S1 pocket, and its carboxyl group is used for cyclization to the P3 lysine residue via an appropriate linker segment. The most potent compounds inhibit the ZIKV protease with K i values between 1.5 - 5 nM. Crystal structures of seven ZIKV protease inhibitor complexes were determined to support the design of the inhibitors. The binding mode of these compounds also explains their high selectivity as NS2B-NS3 inhibitors, which possess a negligible inhibitory effect on trypsin-like serine proteases or furin-like proprotein convertases. Although the WNV and DENV4 proteases are less efficiently inhibited, a comparable ranking of the potencies was observed for all three flavivirins suggesting that this compound type could serve as pan-flaviviral protease inhibitors.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Genome polyproteinB154Zika 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)
Find proteins for Q32ZE1 (Zika virus)
Explore Q32ZE1 
Go to UniProtKB:  Q32ZE1
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Genome polyproteinA38Zika 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)
Find proteins for Q32ZE1 (Zika virus)
Explore Q32ZE1 
Go to UniProtKB:  Q32ZE1
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DUU
Query on DUU

Download CCD File 
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[22.2.2]octacosa-1(26),24,27-trien-10-yl]guanidine
C32 H54 N10 O5
NYYOECQKOMJJPT-NXCFDTQHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.189 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.58α = 90
b = 42.58β = 90
c = 215.26γ = 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: 2019-07-23 
  • 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 

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references