9I7Z | pdb_00009i7z

LecA in complex with 2-fluoro non-carbohydrate glycomimetic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.204 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.168 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The Parkinson's Disease Drug Tolcapone and Analogues are Potent Glycomimetic Lectin Inhibitors of Pseudomonas aeruginosa LecA.

Leusmann, S.Siebs, E.Kuhaudomlarp, S.Varrot, A.Imberty, A.Kuhn, B.Lerner, C.Grether, U.Titz, A.

(2025) Angew Chem Int Ed Engl : e202508864-e202508864

  • DOI: https://doi.org/10.1002/anie.202508864
  • Primary Citation of Related Structures:  
    9I7Z, 9I80

  • PubMed Abstract: 

    The notorious pathogen Pseudomonas aeruginosa relies on the lectin LecA for host cell adhesion, invasion, and biofilm formation. Motivated by the pressing need for new anti-infective therapies caused by antimicrobial resistance, inhibitors of LecA are under investigation. Complementary to the use of carbohydrate-based inhibitors, we have previously identified catechols as weak but specific ligands of LecA, constituting a novel class of non-carbohydrate glycomimetics. By growing the initial millimolar fragment hits, we identified Tolcapone as a promising compound. To gain insight into the structure-activity relationship (SAR) of catechols as LecA binders, more than 3,200 compounds of the Roche in-house library were experimentally screened in a competitive binding assay at three concentrations. Of these, 48 compounds were chosen for further investigation, resulting in compounds equipotent to aryl galactosides, the current epitome of LecA inhibition. X-ray crystallography and saturation transfer difference (STD) NMR spectroscopy revealed conserved interactions of the catechol moiety in the glycan binding site of LecA and rationalized the observed SAR. Our findings demonstrate that it is possible to develop potent non-carbohydrate glycomimetic lectin inhibitors. This work paves the way for a new avenue of research towards innovative anti-infective drugs. In a more general perspective, such small molecules also hold potential to challenge the hegemony of antibodies for lectin inhibition in clinical use.


  • Organizational Affiliation
    • Chemical Biology of Carbohydrates (CBCH), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123, Saarbrücken, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PA-I galactophilic lectin
A, B, C, D
121Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lecApa1LPA2570
UniProt
Find proteins for Q05097 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q05097 
Go to UniProtKB:  Q05097
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05097
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9YU
Query on 9YU

Download Ideal Coordinates CCD File 
P [auth C]2-[2-[2-[2-[2-[2-(2-methoxyethoxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanol
C15 H32 O8
AGWKUHGLWHMYTG-UHFFFAOYSA-N
A1IZM (Subject of Investigation/LOI)
Query on A1IZM

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F [auth A],
L [auth B],
O [auth C],
U [auth D]
[2,6-bis(fluoranyl)phenyl]-[3-nitro-4,5-bis(oxidanyl)phenyl]methanone
C13 H7 F2 N O5
IGCMBTUXZXDHQQ-UHFFFAOYSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
G [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4

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M [auth B],
V [auth D]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

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W [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

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H [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

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Q [auth C]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA (Subject of Investigation/LOI)
Query on CA

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E [auth A],
K [auth B],
N [auth C],
T [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
R [auth C],
S [auth C],
X [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.204 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.168 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.576α = 90
b = 50.728β = 100.011
c = 71.689γ = 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

  • Released Date: 2025-10-22 
  • Deposition Author(s): Varrot, A.

Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-17-CE11-0048
German Research Foundation (DFG)GermanyTi756/5-1

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Database references