8EM8

Co-crystal structure of the cGMP-dependent protein kinase PKG from Plasmodium falciparum in complex with RY-1-165


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structure-Activity Relationship of a Pyrrole Based Series of PfPKG Inhibitors as Anti-Malarials.

Gilleran, J.A.Ashraf, K.Delvillar, M.Eck, T.Fondekar, R.Miller, E.B.Hutchinson, A.Dong, A.Seitova, A.De Souza, M.L.Augeri, D.Halabelian, L.Siekierka, J.Rotella, D.P.Gordon, J.Childers, W.E.Grier, M.C.Staker, B.L.Roberge, J.Y.Bhanot, P.

(2024) J Med Chem 67: 3467-3503

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01795
  • Primary Citation of Related Structures:  
    8EM8

  • PubMed Abstract: 

    Controlling malaria requires new drugs against Plasmodium falciparum . The P. falciparum cGMP-dependent protein kinase (PfPKG) is a validated target whose inhibitors could block multiple steps of the parasite's life cycle. We defined the structure-activity relationship (SAR) of a pyrrole series for PfPKG inhibition. Key pharmacophores were modified to enable full exploration of chemical diversity and to gain knowledge about an ideal core scaffold. In vitro potency against recombinant PfPKG and human PKG were used to determine compound selectivity for the parasite enzyme. P. berghei sporozoites and P. falciparum asexual blood stages were used to assay multistage antiparasitic activity. Cellular specificity of compounds was evaluated using transgenic parasites expressing PfPKG carrying a substituted "gatekeeper" residue. The structure of PfPKG bound to an inhibitor was solved, and modeling using this structure together with computational tools was utilized to understand SAR and establish a rational strategy for subsequent lead optimization.


  • Organizational Affiliation

    Rutgers Molecular Design and Synthesis Core, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cGMP-dependent protein kinase853Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PKGPF3D7_1436600
EC: 2.7.11.12
UniProt
Find proteins for Q8I719 (Plasmodium falciparum (isolate 3D7))
Explore Q8I719 
Go to UniProtKB:  Q8I719
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I719
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
unidentified peptide fragmentB [auth U]4Plasmodium falciparum 3D7Mutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.145α = 90
b = 127.986β = 90
c = 213.728γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-08-07
    Changes: Database references