4TN4

Crystal structure of ternary complex of Plasmodium vivax SHMT with glycine and a novel pyrazolopyran 33G: (4S)-6-amino-4-(5-cyano-3'-fluorobiphenyl-3-yl)-4-cyclobutyl-3-methyl-2,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT): Cocrystal Structures of Pyrazolopyrans with Potent Blood- and Liver-Stage Activities.

Witschel, M.C.Rottmann, M.Schwab, A.Leartsakulpanich, U.Chitnumsub, P.Seet, M.Tonazzi, S.Schwertz, G.Stelzer, F.Mietzner, T.McNamara, C.Thater, F.Freymond, C.Jaruwat, A.Pinthong, C.Riangrungroj, P.Oufir, M.Hamburger, M.Maser, P.Sanz-Alonso, L.M.Charman, S.Wittlin, S.Yuthavong, Y.Chaiyen, P.Diederich, F.

(2015) J.Med.Chem. 58: 3117-3130

  • DOI: 10.1021/jm501987h
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Several of the enzymes related to the folate cycle are well-known for their role as clinically validated antimalarial targets. Nevertheless for serine hydroxymethyltransferase (SHMT), one of the key enzymes of this cycle, efficient inhibitors have no ...

    Several of the enzymes related to the folate cycle are well-known for their role as clinically validated antimalarial targets. Nevertheless for serine hydroxymethyltransferase (SHMT), one of the key enzymes of this cycle, efficient inhibitors have not been described so far. On the basis of plant SHMT inhibitors from an herbicide optimization program, highly potent inhibitors of Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) SHMT with a pyrazolopyran core structure were identified. Cocrystal structures of potent inhibitors with PvSHMT were solved at 2.6 Å resolution. These ligands showed activity (IC50/EC50 values) in the nanomolar range against purified PfSHMT, blood-stage Pf, and liver-stage P. berghei (Pb) cells and a high selectivity when assayed against mammalian cell lines. Pharmacokinetic limitations are the most plausible explanation for lack of significant activity of the inhibitors in the in vivo Pb mouse malaria model.


    Organizational Affiliation

    †BASF SE, Carl-Bosch-Strasse 38, 67056 Ludwigshafen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine hydroxymethyltransferase
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
33G
Query on 33G

Download SDF File 
Download CCD File 
A, B, C
(4S)-6-amino-4-(5-cyano-3'-fluorobiphenyl-3-yl)-4-cyclobutyl-3-methyl-2,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile
C25 H20 F N5 O
NKFOCXNKTOVVHH-VWLOTQADSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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
BME
Query on BME

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Download CCD File 
A, B, C
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.412α = 90.00
b = 57.989β = 89.99
c = 236.955γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
Blu-Icedata collection
PDB_EXTRACTdata extraction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Synchrotron Light Research (Public Organization)ThailandGrant 2551/08
Synchrotron Light Research (Public Organization)ThailandGrant 2-2549/LS01
Cluster Program and Management Office, National Science and Technology development AgencyThailandCPMO-P-13-00835
Cluster Program and Management Office, National Science and Technology development AgencyThailandCPMO-P-00-20029
Cluster Program and Management Office, National Science and Technology development AgencyThailandCPMO-DD/P-10-11274

Revision History 

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-04-01
    Type: Database references
  • Version 1.2: 2015-04-22
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Database references, Derived calculations, Refinement description, Source and taxonomy