4TN4 | pdb_00004tn4

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 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4TN4

Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1021/jm501987h
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 150.25 kDa 
  • Atom Count: 11,035 
  • 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 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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / 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
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
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
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A],
N [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.285 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description