9KP9 | pdb_00009kp9

PfDXR - Mn2+ - NADPH - TAKK443 quaternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 
    0.206 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Expanding the Chemical Space of Reverse Fosmidomycin Analogs.

Knak, T.Takada, S.Illarionov, B.Krisilia, V.Pessanha de Carvalho, L.Lungerich, B.Sakamoto, Y.Hofmann, S.Bacher, A.Kalscheuer, R.Held, J.Fischer, M.Tanaka, N.Kurz, T.

(2025) ACS Med Chem Lett 16: 136-143

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00501
  • Primary Citation Related Structures: 
    8ZXX, 9KP9

  • PubMed Abstract: 

    Multidrug-resistant pathogens pose a major threat to human health, necessitating the identification of new drug targets and lead compounds that are not susceptible to cross-resistance. This study demonstrates that novel reverse thia analogs of the phosphonohydroxamic acid antibiotic fosmidomycin inhibit 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR), an essential enzyme for Plasmodium falciparum , Escherichia coli , and Mycobacterium tuberculosis that is absent in humans. Some novel analogs with large α-phenyl substituents exhibited strong inhibition across these three DXR orthologues, surpassing the inhibitory activity of fosmidomycin. Despite nanomolar target inhibition, the new DXR inhibitors demonstrated mainly weak or no in vitro growth inhibition of the pathogens. Crystallographic studies revealed that compounds 12a and 12b induce an open Pf DXR conformation and that the enzyme selectively binds the S -enantiomers. The study underscores the difficulties of achieving potent cellular activity despite strong DXR inhibition and emphasizes the need for novel structural optimization strategies and comprehensive pharmacokinetic studies.


  • Organizational Affiliation
    • Institute of Pharmaceutical and Medicinal Chemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.

Macromolecule Content 

  • Total Structure Weight: 57.02 kDa 
  • Atom Count: 3,557 
  • Modeled Residue Count: 411 
  • Deposited Residue Count: 488 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic488Plasmodium falciparumMutation(s): 0 
Gene Names: DXR
EC: 1.1.1.267
UniProt
Find proteins for O96693 (Plasmodium falciparum (isolate HB3))
Explore O96693 
Go to UniProtKB:  O96693
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96693
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
(Subject of Investigation/LOI)

Query on NDP



Download:Ideal Coordinates CCD File
B [auth A]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
A1L6A
(Subject of Investigation/LOI)

Query on A1L6A



Download:Ideal Coordinates CCD File
D [auth A][(~{S})-(3-hexoxyphenyl)-[2-[methyl(oxidanyl)amino]-2-oxidanylidene-ethyl]sulfanyl-methyl]phosphonic acid
C16 H26 N O6 P S
YZIQGTUECDVLCI-INIZCTEOSA-N
MN
(Subject of Investigation/LOI)

Query on MN



Download:Ideal Coordinates CCD File
C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free:  0.206 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.498α = 90
b = 92.498β = 90
c = 105.12γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release