5XMQ | pdb_00005xmq

Plasmodium vivax SHMT(C346A) bound with PLP-glycine and MF011


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.276 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5XMQ

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 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.

Macromolecule Content 

  • Total Structure Weight: 150.51 kDa 
  • Atom Count: 11,030 
  • Modeled Residue Count: 1,326 
  • Deposited Residue Count: 1,326 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine hydroxymethyltransferase
A, B, C
442Plasmodium vivaxMutation(s): 1 
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
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8A6

Query on 8A6



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
J [auth C]
4-[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]-~{N}-methyl-~{N}-(phenylmethyl)benzenesulfonamide
C32 H30 F3 N5 O3 S
DBROLDANENNIQJ-HKBQPEDESA-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: 2.20 Å
  • R-Value Free:  0.276 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.319α = 90
b = 58.362β = 90.07
c = 236.453γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



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, Refinement description