7F3Z

Double mutant Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS-K1, C59R+S108N) complexed with Trimethoprim (TOP), NADPH and dUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.198 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances.

Tanramluk, D.Pakotiprapha, D.Phoochaijaroen, S.Chantravisut, P.Thampradid, S.Vanichtanankul, J.Narupiyakul, L.Akavipat, R.Yuvaniyama, J.

(2022) Structure 30: 181-189.e5

  • DOI: https://doi.org/10.1016/j.str.2021.09.004
  • Primary Citation of Related Structures:  
    7F3Y, 7F3Z

  • PubMed Abstract: 

    The MANORAA platform uses structure-based approaches to provide information on drug design originally derived from mapping tens of thousands of amino acids on a grid. In-depth analyses of the pockets, frequently occurring atoms, influential distances, and active-site boundaries are used for the analysis of active sites. The algorithms derived provide model equations that can predict whether changes in distances, such as contraction or expansion, will result in improved binding affinity. The algorithm is confirmed using kinetic studies of dihydrofolate reductase (DHFR), together with two DHFR-TS crystal structures. Empirical analyses of 881 crystal structures involving 180 ligands are used to interpret protein-ligand binding affinities. MANORAA links to major biological databases for web-based analysis of drug design. The frequency of atoms inside the main protease structures, including those from SARS-CoV-2, shows how the rigid part of the ligand can be used as a probe for molecular design (http://manoraa.org).


  • Organizational Affiliation

    Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand; Integrative Computational BioScience (ICBS) Center, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand. Electronic address: duangrudee.tan@mahidol.ac.th.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional dihydrofolate reductase-thymidylate synthase
A, B
608Plasmodium falciparumMutation(s): 0 
Gene Names: dhfr-ts
EC: 2.1.1.45 (UniProt), 1.5.1.3 (UniProt)
UniProt
Find proteins for P13922 (Plasmodium falciparum (isolate K1 / Thailand))
Explore P13922 
Go to UniProtKB:  P13922
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13922
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP (Subject of Investigation/LOI)
Query on NDP

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
UMP (Subject of Investigation/LOI)
Query on UMP

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
TOP (Subject of Investigation/LOI)
Query on TOP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
TRIMETHOPRIM
C14 H18 N4 O3
IEDVJHCEMCRBQM-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.332α = 90
b = 153.739β = 90
c = 164.119γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Derived calculations, Refinement description