5XMV

Plasmodium vivax SHMT bound with PLP-glycine and GS362


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.248 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Conformational Aspects in the Design of Inhibitors for Serine Hydroxymethyltransferase (SHMT): Biphenyl, Aryl Sulfonamide, and Aryl Sulfone Motifs

Schwertz, G.Frei, M.S.Witschel, M.C.Rottmann, M.Leartsakulpanich, U.Chitnumsub, P.Jaruwat, A.Ittarat, W.Schafer, A.Aponte, R.A.Trapp, N.Mark, K.Chaiyen, P.Diederich, F.

(2017) Chemistry 23: 14345-14357

  • DOI: https://doi.org/10.1002/chem.201703244
  • Primary Citation of Related Structures:  
    5XMP, 5XMQ, 5XMR, 5XMS, 5XMT, 5XMU, 5XMV

  • PubMed Abstract: 

    Malaria remains a major threat to mankind due to the perpetual emergence of resistance against marketed drugs. Twenty-one pyrazolopyran-based inhibitors bearing terminal biphenyl, aryl sulfonamide, or aryl sulfone motifs were synthesized and tested towards serine hydroxymethyltransferase (SHMT), a key enzyme of the folate cycle. The best ligands inhibited Plasmodium falciparum (Pf) and Arabidopsis thaliana (At) SHMT in target, as well as PfNF54 strains in cell-based assays in the low nanomolar range (18-56 nm). Seven co-crystal structures with P. vivax (Pv) SHMT were solved at 2.2-2.6 Å resolution. We observed an unprecedented influence of the torsion angle of ortho-substituted biphenyl moieties on cell-based efficacy. The peculiar lipophilic character of the sulfonyl moiety was highlighted in the complexes with aryl sulfonamide analogues, which bind in their preferred staggered orientation. The results are discussed within the context of conformational preferences in the ligands.


  • 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
A, B, C
442Plasmodium vivaxMutation(s): 0 
Gene Names: PVC01_140059500PVP01_1453700PVT01_140059000
EC: 2.1.2.1
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8AU
Query on 8AU

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C]
(4~{S})-6-azanyl-4-[3-(2-chlorophenyl)-5-(trifluoromethyl)phenyl]-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazole-5- carbonitrile
C24 H20 Cl F3 N4 O
MHJHVTMVGRIZDH-QHCPKHFHSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.248 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.674α = 90
b = 58.843β = 90.14
c = 234.899γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science and Technology development AgencyThailandCPMO-P-13-00835
National Center for Genetic Engineering and BiotechnologyThailandPlatform P-14-50241

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary