5YG4

Plasmodium vivax SHMT bound with PLP-glycine and S-GS849


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Potent Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT) Featuring a Spirocyclic Scaffold

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

(2018) ChemMedChem 13: 931-943

  • DOI: 10.1002/cmdc.201800053
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • With the discovery that serine hydroxymethyltransferase (SHMT) is a druggable target for antimalarials, the aim of this study was to design novel inhibitors of this key enzyme in the folate biosynthesis cycle. Herein, 19 novel spirocyclic ligands bas ...

    With the discovery that serine hydroxymethyltransferase (SHMT) is a druggable target for antimalarials, the aim of this study was to design novel inhibitors of this key enzyme in the folate biosynthesis cycle. Herein, 19 novel spirocyclic ligands based on either 2-indolinone or dihydroindene scaffolds and featuring a pyrazolopyran core are reported. Strong target affinities for Plasmodium falciparum (Pf) SHMT (14-76 nm) and cellular potencies in the low nanomolar range (165-334 nm) were measured together with interesting selectivity against human cytosolic SHMT1 (hSHMT1). Four co-crystal structures with Plasmodium vivax (Pv) SHMT solved at 2.2-2.4 Å resolution revealed the key role of the vinylogous cyanamide for anchoring ligands within the active site. The spirocyclic motif in the molecules enforces the pyrazolopyran core to adopt a substantially more curved conformation than that of previous non-spirocyclic analogues. Finally, solvation of the spirocyclic lactam ring of the receptor-bound ligands is discussed.


    Organizational Affiliation

    National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Pathumthani, 12120, Thailand.,Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, 272 Rama VI Road, Bangkok, 10400, Thailand.,Department of Biomolecular Science and Engineering, School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, 21210, Thailand.,BASF SE, Carl-Bosch-Strasse 38, 67056, Ludwigshafen, Germany.,Swiss Tropical and Public Health Institute (SwissTPH), Socinstrasse 57, 4051, Basel, Switzerland.,Universität Basel, Petersplatz 1, 4003, Basel, Switzerland.,Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine hydroxymethyltransferase
A, B, C
442Plasmodium vivaxMutation(s): 0 
EC: 2.1.2.1
Find proteins for A0A1G4H5I1 (Plasmodium vivax)
Go to UniProtKB:  A0A1G4H5I1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8UF
Query on 8UF

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A, B, C
2-[1-[(3~{S})-6'-azanyl-5'-cyano-7-fluoranyl-2,2,3'-trimethyl-spiro[1~{H}-indene-3,4'-2~{H}-pyrano[2,3-c]pyrazole]-5-yl]piperidin-4-yl]ethanoic acid
C25 H28 F N5 O3
IJNFEDVSEBDSHQ-RUZDIDTESA-N
 Ligand Interaction
CL
Query on CL

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A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PLG
Query on PLG

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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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.848α = 90.00
b = 58.207β = 89.99
c = 234.497γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release