2Y1O

Dual-target Inhibitor of MurD and MurE Ligases: Design, Synthesis and Binding Mode Studies

PDB DOI: https://doi.org/10.2210/pdb2Y1O/pdb

Classification: LIGASE
Organism(s): Escherichia coli DH5[alpha]
Expression System: Escherichia coli DH5[alpha]
Mutation(s): No

Deposited: 2010-12-09 Released: 2011-12-28
Deposition Author(s): Tomasic, T., Sink, R., Kovac, A., Turk, S., Contreras-Martel, C., Dessen, A., Blanot, D., Gobec, S., Zega, A., Kikelj, D., Peterlin-Masic, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.228
R-Value Work: 0.205
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Dual Inhibitor of MurD and MurE Ligases from Escherichia coli and Staphylococcus aureus.

Tomasic, T., Sink, R., Zidar, N., Fic, A., Contreras-Martel, C., Dessen, A., Patin, D., Blanot, D., Muller-Premru, M., Gobec, S., Zega, A., Kikelj, D., Masic, L.P.

(2012) ACS Med Chem Lett 3: 626-630

PubMed: 24900523 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/ml300047h
Primary Citation of Related Structures:
2Y1O

PubMed Abstract:
MurD and MurE ligases, consecutive enzymes participating in the intracellular steps of bacterial peptidoglycan biosynthesis, are important targets for antibacterial drug discovery. We have designed, synthesized, and evaluated the first d-glutamic acid-containing dual inhibitor of MurD and MurE ligases from Escherichia coli and Staphylococcus aureus (IC50 values between 6.4 and 180 μM) possessing antibacterial activity against Gram-positive S. aureus and its methicillin-resistant strain (MRSA) with minimal inhibitory concentration (MIC) values of 8 μg/mL. The inhibitor was also found to be noncytotoxic for human HepG2 cells at concentrations below 200 μM.

Organizational Affiliation

Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia.

Macromolecule Content

Total Structure Weight: 49.18 kDa
Atom Count: 3,835
Modelled Residue Count: 435
Deposited Residue Count: 445
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE	A	445	Escherichia coli DH5[alpha]	Mutation(s): 0 EC: 6.3.2.9
UniProt
Find proteins for P14900 (Escherichia coli (strain K12)) Explore P14900 Go to UniProtKB: P14900
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14900
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T26 Query on T26 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	(2R)-2-[[3-[[4-[(Z)-(4-OXO-2-SULFANYLIDENE-1,3-THIAZOLIDIN-5-YLIDENE)METHYL]PHENYL]METHYLAMINO]PHENYL]CARBONYLAMINO]PENTANEDIOIC ACID C₂₃ H₂₁ N₃ O₆ S₂ ZDOPULPHJIBVJX-RMFUMNGISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A]	G [auth A], H [auth A], I [auth A], J [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Binding Affinity Annotations
ID	Source	Binding Affinity
T26	PDBBind: 2Y1O	IC50: 8200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.228
R-Value Work: 0.205
R-Value Observed: 0.207
Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.844	α = 90
b = 65.844	β = 90
c = 135.747	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-12-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-12-28
Type: Initial release
Version 1.1: 2013-02-27
Changes: Database references
Version 1.2: 2017-12-20
Changes: Database references
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description