7ZST

Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum in complex with FLA-01


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.236 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Discovery of Small-Molecule Allosteric Inhibitors of Pf ATC as Antimalarials.

Wang, C.Zhang, B.Kruger, A.Du, X.Visser, L.Domling, A.S.S.Wrenger, C.Groves, M.R.

(2022) J Am Chem Soc 144: 19070-19077

  • DOI: https://doi.org/10.1021/jacs.2c08128
  • Primary Citation of Related Structures:  
    7ZCZ, 7ZEA, 7ZGS, 7ZHI, 7ZID, 7ZP2, 7ZST

  • PubMed Abstract: 

    The discovery and development of new drugs against malaria remain urgent. Aspartate transcarbamoylase (ATC) has been suggested to be a promising target for antimalarial drug development. Here, we describe a series of small-molecule inhibitors of P. falciparum ATC with low nanomolar binding affinities that selectively bind to a previously unreported allosteric pocket, thereby inhibiting ATC activation. We demonstrate that the buried allosteric pocket is located close to the traditional ATC active site and that reported compounds maintain the active site of Pf ATC in its low substrate affinity/low activity conformation. These compounds inhibit parasite growth in blood stage cultures at single digit micromolar concentrations, whereas limited effects were seen against human normal lymphocytes. To our knowledge, this series represent the first Pf ATC-specific allosteric inhibitors.


  • Organizational Affiliation

    XB20 Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate carbamoyltransferase
A, B, C
349Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1344800
EC: 2.1.3.2
UniProt
Find proteins for A0A5K1K910 (Plasmodium falciparum (isolate 3D7))
Explore A0A5K1K910 
Go to UniProtKB:  A0A5K1K910
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5K1K910
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JUF (Subject of Investigation/LOI)
Query on JUF

Download Ideal Coordinates CCD File 
H [auth B]2-azanyl-~{N}-(2-methoxyethyl)-5-phenyl-thiophene-3-carboxamide
C14 H16 N2 O2 S
QOTMPSXFERGPKP-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.236 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.284α = 90
b = 89.735β = 109.215
c = 137.052γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Scholarship CouncilChina--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2022-09-07
    Changes: Structure summary
  • Version 1.2: 2022-10-26
    Changes: Database references
  • Version 1.3: 2022-11-02
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Data collection, Refinement description