8AIJ | pdb_00008aij

STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PAO1 IN COMPLEX WITH N-(alpha-L-Fucopyranosyl)benzamide (6)

PDB DOI: https://doi.org/10.2210/pdb8AIJ/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-26 Released: 2022-11-02
Deposition Author(s): Meiers, J., Mala, P., Varrot, A., Siebs, E., Imberty, A., Titz, A.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.169 (Depositor), 0.183 (DCC)
R-Value Work:
0.138 (Depositor)

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

Discovery of N -beta-l-Fucosyl Amides as High-Affinity Ligands for the Pseudomonas aeruginosa Lectin LecB.

Mala, P., Siebs, E., Meiers, J., Rox, K., Varrot, A., Imberty, A., Titz, A.

(2022) J Med Chem 65: 14180-14200

PubMed: 36256875 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.2c01373
Primary Citation Related Structures:
8AIJ, 8AIY

PubMed Abstract:
The Gram-negative pathogen Pseudomonas aeruginosa causes severe infections mainly in immunocompromised or cystic fibrosis patients and is able to resist antimicrobial treatments. The extracellular lectin LecB plays a key role in bacterial adhesion to the host and biofilm formation. For the inhibition of LecB, we designed and synthesized a set of fucosyl amides, sulfonamides, and thiourea derivatives. Then, we analyzed their binding to LecB in competitive and direct binding assays. We identified β-fucosyl amides as unprecedented high-affinity ligands in the two-digit nanomolar range. X-ray crystallography of one α- and one β-anomer of N -fucosyl amides in complex with LecB revealed the interactions responsible for the high affinity of the β-anomer at atomic level. Further, the molecules showed good stability in murine and human blood plasma and hepatic metabolism, providing a basis for future development into antibacterial drugs.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 48.58 kDa
Atom Count: 4,065
Modeled Residue Count: 456
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin PA-IIL	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	114	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: lecB, PA3361
UniProt
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HYN5 Go to UniProtKB: Q9HYN5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HYN5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M9I (Subject of Investigation/LOI) Query on M9I Download:Ideal Coordinates CCD File SDF format, chain T [auth DDD] SDF format, chain Q [auth CCC] SDF format, chain M [auth BBB] SDF format, chain G [auth AAA] MOL2 format, chain T [auth DDD] MOL2 format, chain Q [auth CCC] MOL2 format, chain M [auth BBB] MOL2 format, chain G [auth AAA] mmCIF format, chain T [auth DDD] mmCIF format, chain Q [auth CCC] mmCIF format, chain M [auth BBB] mmCIF format, chain G [auth AAA]	G [auth AAA], M [auth BBB], Q [auth CCC], T [auth DDD]	N-(alpha-L-Fucopyranosyl)benzamide C₁₃ H₁₇ N O₅ ZYWNMRPOYLXAAW-HTUCIKCGSA-N		Interactions Focus chain G [auth AAA] Focus chain M [auth BBB] Focus chain Q [auth CCC] Focus chain T [auth DDD] Interactions & Density Focus chain G [auth AAA] Focus chain M [auth BBB] Focus chain Q [auth CCC] Focus chain T [auth DDD]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth BBB] SDF format, chain J [auth AAA] SDF format, chain I [auth AAA] SDF format, chain H [auth AAA] MOL2 format, chain N [auth BBB] MOL2 format, chain J [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain H [auth AAA] mmCIF format, chain N [auth BBB] mmCIF format, chain J [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain H [auth AAA]	H [auth AAA], I [auth AAA], J [auth AAA], N [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain N [auth BBB] Interactions & Density Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain N [auth BBB]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain O [auth CCC] SDF format, chain S [auth DDD] SDF format, chain R [auth DDD] SDF format, chain P [auth CCC] SDF format, chain L [auth BBB] SDF format, chain K [auth BBB] SDF format, chain F [auth AAA] SDF format, chain E [auth AAA] MOL2 format, chain O [auth CCC] MOL2 format, chain S [auth DDD] MOL2 format, chain R [auth DDD] MOL2 format, chain P [auth CCC] MOL2 format, chain L [auth BBB] MOL2 format, chain K [auth BBB] MOL2 format, chain F [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain O [auth CCC] mmCIF format, chain S [auth DDD] mmCIF format, chain R [auth DDD] mmCIF format, chain P [auth CCC] mmCIF format, chain L [auth BBB] mmCIF format, chain K [auth BBB] mmCIF format, chain F [auth AAA] mmCIF format, chain E [auth AAA]	E [auth AAA] F [auth AAA] K [auth BBB] L [auth BBB] O [auth CCC] E [auth AAA], F [auth AAA], K [auth BBB], L [auth BBB], O [auth CCC], P [auth CCC], R [auth DDD], S [auth DDD]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain K [auth BBB] Focus chain L [auth BBB] Focus chain O [auth CCC] Focus chain P [auth CCC] Focus chain R [auth DDD] Focus chain S [auth DDD] Interactions & Density Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain K [auth BBB] Focus chain L [auth BBB] Focus chain O [auth CCC] Focus chain P [auth CCC] Focus chain R [auth DDD] Focus chain S [auth DDD]