5ZMQ

Crystal structure of Zika NS3 protease with phenylacetyl-Lys-Lys-Arg-COOH inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.987 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of Zika virus NS2B-NS3 protease in complex with peptidomimetic inhibitors.

Phoo, W.W.Zhang, Z.Wirawan, M.Chew, E.J.C.Chew, A.B.L.Kouretova, J.Steinmetzer, T.Luo, D.

(2018) Antiviral Res. 160: 17-24

  • DOI: 10.1016/j.antiviral.2018.10.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Zika virus NS2B-NS3 protease plays an essential role in viral replication by processing the viral polyprotein into individual proteins. The viral protease is therefore considered as an ideal antiviral drug target. To facilitate the development of pro ...

    Zika virus NS2B-NS3 protease plays an essential role in viral replication by processing the viral polyprotein into individual proteins. The viral protease is therefore considered as an ideal antiviral drug target. To facilitate the development of protease inhibitors, we report three high-resolution co-crystal structures of bZiPro with peptidomimetic inhibitors composed of a P1-P4 segment and different P1' residues. Compounds 1 and 2 possess small P1' groups that are split off by bZiPro, which could be detected by mass spectrometry. On the other hand, the more potent compound 3 contains a bulky P1' benzylamide structure that is resistant to cleavage by bZiPro, demonstrating that presence of an uncleavable C-terminal cap contributes to a slightly improved inhibitory potency. The N-terminal phenylacetyl residue occupies a position above the P1 side chain and therefore stabilizes a horseshoe-like backbone conformation of the bound inhibitors. The P4 moieties show unique intra- and intermolecular interactions. Our work reports the detailed binding mode interactions of substrate-analogue inhibitors within the S4-S1' pockets and explains the preference of bZiPro for basic P1-P3 residues. These new structures of protease-inhibitor complexes will guide the design of more effective NS2B-NS3 protease inhibitors with improved potency and bioavailability.


    Organizational Affiliation

    Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine protease subunit NS2B
A, C, E, G
53Zika virusMutation(s): 0 
Find proteins for Q32ZE1 (Zika virus)
Go to UniProtKB:  Q32ZE1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Serine protease NS3
B, D, F, H
178Zika virusMutation(s): 1 
Find proteins for Q32ZE1 (Zika virus)
Go to UniProtKB:  Q32ZE1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
peptide PAC-DLY-DLY-DAR
I, K
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002309
Query on PRD_002309
I,KN2-(phenylacetyl)-D-lysyl-D-lysyl-D-argininePeptide-like / Enzyme inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.987 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.150α = 90.00
b = 60.330β = 90.00
c = 214.070γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Singaporestart up grant
SingaporeCBRG15May045
SingaporeNRF2016NRF-CRP001-063
Ministry of Education (Singapore)SingaporeMOE2016-T2-2-097
GermanyDZIF-TTU 01.902

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-10-31
    Type: Data collection, Database references