8WGM

Quadruple mutant Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S, N51I+C59R+S108N+I164L) complexed with LA1, NADPH and dUMP

• PDB DOI: https://doi.org/10.2210/pdb8WGM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Plasmodium falciparum VS/1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-09-22 Released: 2024-09-11 
• Deposition Author(s): Vanichtanankul, J., Saeyang, T., Vitsupakorn, D., Arwon, U., Decharuangsilp, S., Yuthavong, Y., Kamchonwongpaisan, S.
• Funding Organization(s): National Science and Technology Development Agency (NSTDA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.233 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

Flexible 2,4-diaminopyrimidine bearing a butyrolactone as Plasmodium falciparum dihydrofolate reductase inhibitors

Decharuangsilp, S., Arwon, U., Hoarau, M., Vanichtanankul, J., Saeyang, T., Jantra, T., Rattanajak, R., Thiabma, R., Sooksai, N., Kongkasuriyachai, D., Kamchonwongpaisan, S., Yuthavong, Y.

(2024) Bioorg Chem 

• DOI: https://doi.org/10.1016/j.bioorg.2024.107789

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 146.49 kDa 
• Atom Count: 9,780 
• Modelled Residue Count: 1,060 
• Deposited Residue Count: 1,216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional dihydrofolate reductase-thymidylate synthase	A, B	608	Plasmodium falciparum VS/1	Mutation(s): 4  Gene Names: DHFR-TS
UniProt
Find proteins for A7UD81 (Plasmodium falciparum) Explore A7UD81  Go to UniProtKB:  A7UD81

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], F [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
WCQ (Subject of Investigation/LOI)	E [auth A], H [auth B]	(3~{E})-3-[[2-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]oxypropoxy]phenyl]methylidene]oxolan-2-one C20 H24 N4 O4 IYGGQEQHKUVGBG-WYMLVPIESA-N
UMP	D [auth A], G [auth B]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.233 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.355	α = 90
b = 156.283	β = 90
c = 165	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
PROTEUM PLUS	data collection
PROTEUM PLUS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Vanichtanankul, J., Saeyang, T., Vitsupakorn, D., Arwon, U., Decharuangsilp, S., Yuthavong, Y., Kamchonwongpaisan, S.

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Funding Organization	Location	Grant Number
National Science and Technology Development Agency (NSTDA)	Thailand	P1850116

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release