5GVK

Plasmodium vivax SHMT bound with PLP-glycine and GS256


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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:  

  • 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 (t1/2 > 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine hydroxymethyltransferase, putative
A, B, C
442Plasmodium vivax (strain Salvador I)Mutation(s): 0 
Find proteins for A5K8L9 (Plasmodium vivax (strain Salvador I))
Go to UniProtKB:  A5K8L9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PLG
Query on PLG

Download SDF File 
Download CCD File 
A, B, C
N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE
C10 H15 N2 O7 P
FEVQWBMNLWUBTF-UHFFFAOYSA-N
 Ligand Interaction
G45
Query on G45

Download SDF File 
Download CCD File 
A, B, C
5-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-cyano-phenyl]-~{N},~{N}-dimethyl-thiophene-2-sulfonamide
C24 H24 N6 O3 S2
KSCQEXGCEZGBHT-DEOSSOPVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.943α = 90.00
b = 58.297β = 90.02
c = 233.613γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Blu-Icedata collection
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



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