7ZVS | pdb_00007zvs

Crystal structure of the Schistosoma mansoni VKR2 kinase domain in an active-like state (ADP-bound)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 
    0.252 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Identification of Inhibitors of the Schistosoma mansoni VKR2 Kinase Domain.

Mathavan, I.Liu, L.J.Robinson, S.W.El-Sakkary, N.Elatico, A.J.J.Gomez, D.Nellas, R.Owens, R.J.Zuercher, W.Navratilova, I.Caffrey, C.R.Beis, K.

(2022) ACS Med Chem Lett 13: 1715-1722

  • DOI: https://doi.org/10.1021/acsmedchemlett.2c00248
  • Primary Citation Related Structures: 
    7ZVS

  • PubMed Abstract: 

    Schistosomiasis is a neglected tropical disease caused by parasitic flatworms. Current treatment relies on just one partially effective drug, praziquantel (PZQ). Schistosoma mansoni Venus Kinase Receptors 1 and 2 (SmVKR1 and SmVKR2) are important for parasite growth and egg production, and are potential targets for combating schistosomiasis. VKRs consist of an extracellular Venus Flytrap Module (VFTM) linked via a transmembrane helix to a kinase domain. Here, we initiated a drug discovery effort to inhibit the activity of the SmVKR2 kinase domain (SmVKR2 KD ) by screening the GSK published kinase inhibitor set 2 (PKIS2). We identified several inhibitors, of which four were able to inhibit its enzymatic activity and induced phenotypic changes in ex vivo S. mansoni . Our crystal structure of the SmVKR2 KD displays an active-like state that sheds light on the activation process of VKRs. Our data provide a basis for the further exploration of SmVKR2 as a possible drug target.


  • Organizational Affiliation
    • Department of Life Sciences, Imperial College London, Exhibition Road, London, South Kensington SW7 2AZ, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 117.27 kDa 
  • Atom Count: 7,186 
  • Modeled Residue Count: 896 
  • Deposited Residue Count: 1,023 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Venus kinase receptor 2
A, B, C
341Schistosoma mansoniMutation(s): 0 
UniProt
Find proteins for A0A3Q0KQ92 (Schistosoma mansoni)
Explore A0A3Q0KQ92 
Go to UniProtKB:  A0A3Q0KQ92
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3Q0KQ92
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free:  0.252 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 206.258α = 90
b = 97.239β = 97.52
c = 72.944γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/N019113/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2022-11-30
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description