9IBY | pdb_00009iby

Crystal structure of Zika Virus NS2B-NS3 protease in complex with compound 2

• PDB DOI: https://doi.org/10.2210/pdb9IBY/pdb

• Classification: HYDROLASE
• Organism(s): Zika virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-02-14 Released: 2025-12-03 
• Deposition Author(s): Ontario, J.M., Torrente, E.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.195 (DCC) 

Starting Model: experimental

Literature

Crystal structure of Zika Virus NS2B-NS3 protease in complex with compounds to be submitted

Ontoria, J.M., Torrente, E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.83 kDa 
• Atom Count: 2,608 
• Modeled Residue Count: 324 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, B	230	Zika virus	Mutation(s): 0
UniProt
Find proteins for A0A140DLX4 (Zika virus) Explore A0A140DLX4  Go to UniProtKB:  A0A140DLX4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1I16 (Subject of Investigation/LOI)	C [auth A], E [auth B]	1-[3-[[5-(4,6-dimethylpyrimidin-5-yl)pyridin-2-yl]methyl]-1-oxa-2,3$l^{4}-diazacyclopenta-2,4-dien-5-yl]-3-[3-(trifluoromethyl)phenyl]urea C22 H19 F3 N7 O2 JJQASPUODGTFMB-UHFFFAOYSA-O
ACY	D [auth A], F [auth B], G [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAF	A, B	L-PEPTIDE LINKING	C5 H12 As N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.195 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.793	α = 90
b = 57.472	β = 96.406
c = 72.447	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Ontario, J.M., Torrente, E.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release