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: 2.20 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.224 

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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:  
    4TMR, 4TN4

  • 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 not been described so far ...

    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: 

    ∥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
MoleculeChainsSequence LengthOrganismDetailsImage
Serine hydroxymethyltransferaseA, B, C442Plasmodium vivax Sal-1Mutation(s): 0 
Gene Names: PVX_100730
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
33G
Query on 33G
Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth 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
PLG
Query on PLG
Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
K [auth C]		N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
C10 H15 N2 O7 P
FEVQWBMNLWUBTF-UHFFFAOYSA-N		 Ligand Interaction
BME
Query on BME
Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C]		BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
G [auth A],
N [auth C]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.412α = 90
b = 57.989β = 89.99
c = 236.955γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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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  (Full details and data files)

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