7ZNO | pdb_00007zno

Crystal Structure of Unlinked NS2B_NS3 Protease from Zika Virus in Complex with Boronate Inhibitor MI-2270

• PDB DOI: https://doi.org/10.2210/pdb7ZNO/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Zika virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-04-21 Released: 2022-06-22 
• Deposition Author(s): Huber, S., Heine, A., Steinmetzer, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.225 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Boroleucine-Derived Covalent Inhibitors of the ZIKV Protease.

Braun, N.J., Huber, S., Schmacke, L.C., Heine, A., Steinmetzer, T.

(2023) ChemMedChem 18: e202200336-e202200336

• PubMed: 36325810 
• DOI: https://doi.org/10.1002/cmdc.202200336
• Primary Citation Related Structures: 
  7ZNO


• PubMed Abstract: 
  

  The Zika virus (ZIKV) remains a potential threat to the public health due to the lack of both an approved vaccination or a specific treatment. In this work, a series of peptidic inhibitors of the ZIKV protease with boroleucine as P1 residue was synthesized. The highest affinities with K _i values down to 8 nM were observed for compounds with basic residues in both P2 and P3 position and at the N-terminus. The low potency of reference compounds containing leucine, leucine-amide or isopentylamide as P1 residue suggested a covalent binding mode of the boroleucine-derived inhibitors. This was finally proven by crystal structure determination of the most potent inhibitor from this series in complex with the ZIKV protease.

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Organizational Affiliation: 
• Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.55 kDa 
• Atom Count: 1,513 
• Modeled Residue Count: 193 
• Deposited Residue Count: 231 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease subunit NS2B	A	53	Zika virus	Mutation(s): 0
UniProt
Find proteins for Q32ZE1 (Zika virus) Explore Q32ZE1  Go to UniProtKB:  Q32ZE1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease NS3	B	178	Zika virus	Mutation(s): 0  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) Explore Q32ZE1  Go to UniProtKB:  Q32ZE1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JQI (Subject of Investigation/LOI)	C [auth B]	[(1R)-1-[[(2S)-6-azanyl-2-[[(2S)-6-azanyl-2-[2-[3-(4-carbamimidamido-3-oxidanylidene-pentyl)phenyl]ethanoylamino]hexanoyl]amino]hexanoyl]amino]-3-methyl-butyl]boronic acid C31 H55 B N8 O6 CMFRRGVPVDGVRV-QUCWNPHKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.225 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.397	α = 90
b = 42.397	β = 90
c = 215.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Huber, S., Heine, A., Steinmetzer, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2022-12-28
  Changes: Database references
• Version 1.2: 2023-02-15
  Changes: Database references
• Version 1.3: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary