7IAS | pdb_00007ias

Crystal structure of Zika NS2B-NS3 protease in complex with fragment EOS102659 from ECBL-96


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

From fragments to follow-ups: rapid hit expansion by making use of EU-OPENSCREEN resources.

Benz, L.S.Wollenhaupt, J.Jirgensons, A.Miletic, T.Mueller, U.Weiss, M.S.

(2025) RSC Med Chem 

  • DOI: https://doi.org/10.1039/d5md00684h
  • Primary Citation of Related Structures:  
    7IAQ, 7IAR, 7IAS, 7IAT, 7IAU, 7IAV, 7IAW, 7IAX, 7IAY, 7IAZ, 7IB0, 7IB1, 7IB2, 7IB3, 7IB4, 7IB5, 7IB6, 7IB7, 7IEP, 7IEQ, 7IER, 7IES, 7IET, 7IEU, 7IEV, 7IEW, 7IEX, 7IEY, 7IEZ, 7IF0, 7IF1, 7IF2, 7IF3, 7IF4, 7IF5, 7IF6, 7IF7, 7IF8, 7IF9, 7IFA, 7IFB, 7IFC, 7IFD, 7IFE, 7IFF, 7IFG, 7IFH, 7IFI, 7IFJ, 7IFK

  • PubMed Abstract: 

    Quite frequently, it is the progression of initial crystallographic fragment screening hits into more potent binders to their target, which constitutes the major bottleneck in many academic compound or drug development projects. While high quality starting points are critical to the success of a drug development project, it is equally important to have accessible pathways for further compound development. Here, we present two crystallographic fragment screening campaigns using a 96 fragment sub-selection of the European Fragment Screening Library (EFSL) provided by EU-OPENSCREEN. The two campaigns against the targets endothiapepsin and the NS2B-NS3 Zika protease, yielded hit rates of 31% and 18%, respectively. Further, we present how within the framework of the EU-OPENSCREEN European Research Infrastructure Consortium (ERIC) fast identification of follow-up compounds can be realized. With just one round of testing related compounds from the European Chemical Biology Library, two follow-up binders for each of the two targets could be identified proving the feasibility of this approach.


  • Organizational Affiliation
    • Macromolecular Crystallography, Helmholtz-Zentrum Berlin Albert-Einstein-Str. 15 12489 Berlin Germany manfred.weiss@helmholtz-berlin.de.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NS2B co-factor
A, C
53Zika virusMutation(s): 0 
Gene Names: GP1A2G93_63394gpGP1
UniProt
Find proteins for A0A142IX72 (Zika virus)
Explore A0A142IX72 
Go to UniProtKB:  A0A142IX72
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A142IX72
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NS3 protease
B, D
176Zika virusMutation(s): 1 
Gene Names: GP1A2G93_63394gpGP1
UniProt
Find proteins for A0A142IX72 (Zika virus)
Explore A0A142IX72 
Go to UniProtKB:  A0A142IX72
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A142IX72
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CD0 (Subject of Investigation/LOI)
Query on A1CD0

Download Ideal Coordinates CCD File 
E [auth D]5-methylfuran-2-carboxamide
C6 H7 N O2
HTLIXYXARPLOIU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.31α = 90
b = 60.31β = 90
c = 214.45γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyFE2166/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release