Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 52.29 kDa 
• Atom Count: 3919 
• Modelled Residue Count: 454 
• Deposited Residue Count: 465 
• Unique protein chains: 1

3ZM6

CRYSTAL STRUCTURE OF MURF LIGASE IN COMPLEX WITH CYANOTHIOPHENE INHIBITOR

• PDB DOI: 10.2210/pdb3ZM6/pdb

• Classification: LIGASE
• Organism(s): Streptococcus pneumoniae R6
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2013-02-05 Released: 2013-07-03 
• Deposition Author(s): Hrast, M., Turk, S., Sosic, I., Knez, D., Randall, C.P., Barreteau, H., Contreras-Martel, C., Dessen, A., ONeill, A.J., Mengin-Lecreulx, D., Blanot, D., Gobec, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.255 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 

Literature

Structure-Activity Relationships of New Cyanothiophene Inhibitors of the Essential Peptidoglycan Biosynthesis Enzyme Murf.

Hrast, M., Turk, S., Sosic, I., Knez, D., Randall, C.P., Barreteau, H., Contreras-Martel, C., Dessen, A., O'Neill, A.J., Mengin-Lecreulx, D., Blanot, D., Gobec, S.

(2013) Eur J Med Chem 66C: 32

• PubMed: 23786712 
• DOI: 10.1016/j.ejmech.2013.05.013
• Primary Citation of Related Structures:  
  3ZM5, 3ZM6


• PubMed Abstract: 
  

Peptidoglycan is an essential component of the bacterial cell wall, and enzymes involved in its biosynthesis represent validated targets for antibacterial drug discovery. MurF catalyzes the final intracellular peptidoglycan biosynthesis step: the addition of D-Ala-D-Ala to the nucleotide precursor UDP-MurNAc-L-Ala-γ-D-Glu-meso-DAP (or L-Lys). As MurF has no human counterpart, it represents an attractive target for the development of new antibacterial drugs. Using recently published cyanothiophene inhibitors of MurF from Streptococcus pneumoniae as a starting point, we designed and synthesized a series of structurally related derivatives and investigated their inhibition of MurF enzymes from different bacterial species. Systematic structural modifications of the parent compounds resulted in a series of nanomolar inhibitors of MurF from S. pneumoniae and micromolar inhibitors of MurF from Escherichia coli and Staphylococcus aureus. Some of the inhibitors also show antibacterial activity against S. pneumoniae R6. These findings, together with two new co-crystal structures, represent an excellent starting point for further optimization toward effective novel antibacterials.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE	A	465	Streptococcus pneumoniae R6	Mutation(s): 0  Gene Names: murF, spr1514 EC: 6.3.2.10
UniProt
Find proteins for Q8DNV6 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DNV6  Go to UniProtKB:  Q8DNV6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2GN	B [auth A]	N-(6-(4-(2h-tetrazol-5-yl)benzyl)-3-cyano-4,5,6,7-tetrahydrothieno[2,3-c]pyridin-2-yl)-2,4-dichloro-5-(morpholinosulfonyl)benzamide C27 H24 Cl2 N8 O4 S2 KXJHJZRFLLSTJD-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2GN	Binding MOAD:  3ZM6	IC50: 300 (nM) from 1 assay(s)
	PDBBind:  3ZM6	IC50: 300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.255 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.156	α = 90
b = 116.156	β = 90
c = 160.294	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-05 
• Released Date: 2013-07-03 
Deposition Author(s): Hrast, M., Turk, S., Sosic, I., Knez, D., Randall, C.P., Barreteau, H., Contreras-Martel, C., Dessen, A., ONeill, A.J., Mengin-Lecreulx, D., Blanot, D., Gobec, S.

Revision History  

• Version 1.0: 2013-07-03
  Type: Initial release