2X5O

Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- thiazolidine-2,4-dione Inhibitors of MurD Ligase

• PDB DOI: https://doi.org/10.2210/pdb2X5O/pdb

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


• Deposited: 2010-02-10 Released: 2010-09-15 
• Deposition Author(s): Zidar, N., Tomasic, T., Sink, R., Rupnik, V., Kovac, A., Turk, S., Contreras-Martel, C., Dessen, A., Blanot, D., Gobec, S., Zega, A., Peterlin-Masic, L., Kikelja, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 
  0.217 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Discovery of novel 5-benzylidenerhodanine and 5-benzylidenethiazolidine-2,4-dione inhibitors of MurD ligase.

Zidar, N., Tomasic, T., Sink, R., Rupnik, V., Kovac, A., Turk, S., Patin, D., Blanot, D., Contreras Martel, C., Dessen, A., Muller Premru, M., Zega, A., Gobec, S., Peterlin Masic, L., Kikelj, D.

(2010) J Med Chem 53: 6584-6594

• PubMed: 20804196 
• DOI: https://doi.org/10.1021/jm100285g
• Primary Citation of Related Structures:  
  2WJP, 2X5O


• PubMed Abstract: 
  

  We have designed, synthesized, and evaluated 5-benzylidenerhodanine- and 5-benzylidenethiazolidine-2,4-dione-based compounds as inhibitors of bacterial enzyme MurD with E. coli IC(50) in the range 45-206 μM. The high-resolution crystal structure of MurD in complex with (R,Z)-2-(3-[{4-([2,4-dioxothiazolidin-5-ylidene]methyl)phenylamino}methyl)benzamido)pentanedioic acid [(R)-32] revealed details of the binding mode of the inhibitor within the active site and provides a good foundation for structure-based design of a novel generation of MurD inhibitors.

---

Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.1 kDa 
• Atom Count: 4,012 
• Modelled Residue Count: 439 
• Deposited Residue Count: 439 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE	A	439	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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VSV	B [auth A]	N-({3-[({4-[(Z)-(2,4-DIOXO-1,3-THIAZOLIDIN-5-YLIDENE)METHYL]PHENYL}AMINO)METHYL]PHENYL}CARBONYL)-D-GLUTAMIC ACID C23 H21 N3 O7 S YITBSJALJWUAQA-LVSMMTLPSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
SO3	F [auth A]	SULFITE ION O3 S LSNNMFCWUKXFEE-UHFFFAOYSA-L
AZI	C [auth A]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N
CL	G [auth A], H [auth A], I [auth A], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free:  0.217 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.091	α = 90
b = 66.091	β = 90
c = 135.781	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Zidar, N., Tomasic, T., Sink, R., Rupnik, V., Kovac, A., Turk, S., Contreras-Martel, C., Dessen, A., Blanot, D., Gobec, S., Zega, A., Peterlin-Masic, L., Kikelja, D.

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-08-31
  Changes: Database references, Refinement description, Version format compliance
• Version 1.2: 2018-02-28
  Changes: Database references, Source and taxonomy
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description