5GVM

Plasmodium vivax SHMT bound with PLP-glycine and GS557


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report



Literature

Antimalarial Inhibitors Targeting Serine Hydroxymethyltransferase (SHMT) with in Vivo Efficacy and Analysis of their Binding Mode Based on X-ray Cocrystal Structures

Schwertz, G.Witschel, M.C.Rottmann, M.Bonnert, R.Leartsakulpanich, U.Chitnumsub, P.Jaruwat, A.Ittarat, W.Schafer, A.Aponte, R.A.Charman, S.A.White, K.L.Kundu, A.Sadhukhan, S.Lloyd, M.Freiberg, G.M.Srikumaran, M.Siggel, M.Zwyssig, A.Chaiyen, P.Diederich, F.

(2017) J Med Chem 60: 4840-4860

  • DOI: 10.1021/acs.jmedchem.7b00008
  • Primary Citation of Related Structures:  
    5GVM, 5GVL, 5GVN, 5GVP, 5GVK

  • PubMed Abstract: 
  • Target-based approaches toward new antimalarial treatments are highly valuable to prevent resistance development. We report several series of pyrazolopyran-based inhibitors targeting the enzyme serine hydroxymethyltransferase (SHMT), designed to impr ...

    Target-based approaches toward new antimalarial treatments are highly valuable to prevent resistance development. We report several series of pyrazolopyran-based inhibitors targeting the enzyme serine hydroxymethyltransferase (SHMT), designed to improve microsomal metabolic stability and to identify suitable candidates for in vivo efficacy evaluation. The best ligands inhibited Plasmodium falciparum (Pf) and Arabidopsis thaliana (At) SHMT in target assays and PfNF54 strains in cell-based assays with values in the low nanomolar range (3.2-55 nM). A set of carboxylate derivatives demonstrated markedly improved in vitro metabolic stability (t 1/2 > 2 h). A selected ligand showed significant in vivo efficacy with 73% of parasitemia reduction in a mouse model. Five new cocrystal structures with PvSHMT were solved at 2.3-2.6 Å resolution, revealing a unique water-mediated interaction with Tyr63 at the end of the para-aminobenzoate channel. They also displayed the high degree of conformational flexibility of the Cys364-loop lining this channel.


    Organizational Affiliation

    Laboratorium für Organische Chemie, ETH Zurich , Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine hydroxymethyltransferase, putativeABC442Plasmodium vivax Sal-1Mutation(s): 0 
Gene Names: PVX_100730
EC: 2.1.2.1
Find proteins for A5K8L9 (Plasmodium vivax (strain Salvador I))
Explore A5K8L9 
Go to UniProtKB:  A5K8L9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G57
Query on G57

Download CCD File 
A, B, C
2-[3-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-(trifluoromethyl)phenyl]phenyl]ethanoic acid
C26 H23 F3 N4 O3
DBCDVNKPJCGLLK-VWLOTQADSA-N
 Ligand Interaction
PLG
Query on PLG

Download CCD File 
A, B, C
N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
C10 H15 N2 O7 P
FEVQWBMNLWUBTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G57IC50:  186   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.246 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.858α = 90
b = 58.79β = 90.03
c = 234.062γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science and Technology Development AgencyThailand--

Revision History 

  • Version 1.0: 2017-07-12
    Type: Initial release