5GVL

Plasmodium vivax SHMT bound with PLP-glycine and GS182


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1021/acs.jmedchem.7b00008
  • Primary Citation of Related Structures:  
    5GVK, 5GVL, 5GVM, 5GVN, 5GVP

  • 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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine hydroxymethyltransferase, putative
A, B, C
442Plasmodium vivax Sal-1Mutation(s): 0 
Gene Names: PVX_100730
UniProt
Find proteins for A5K8L9 (Plasmodium vivax (strain Salvador I))
Explore A5K8L9 
Go to UniProtKB:  A5K8L9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5K8L9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GI8
Query on GI8

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C]
(4~{S})-6-azanyl-4-[3-cyano-5-[5-(methoxymethyl)thiophen-2-yl]phenyl]-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazole-5-carbonitrile
C24 H23 N5 O2 S
DRGJPMMQBOXCQB-DEOSSOPVSA-N
PLG
Query on PLG

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

Download Ideal Coordinates CCD File 
F [auth A],
K [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
GI8 Binding MOAD:  5GVL IC50: 42 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.262α = 90
b = 58.506β = 90.04
c = 233.5γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science and Technology Development AgencyThailand--

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description