Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 48.74 kDa 
• Atom Count: 3777 
• Residue Count: 440 
• Unique protein chains: 1

2UUP

Crystal structure of MurD ligase in complex with D-Glu containing sulfonamide inhibitor

• DOI: 10.2210/pdb2UUP/pdb

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


• Deposited: 2007-03-06 Released: 2008-03-25 
• Deposition Author(s): Humljan, J., Kotnik, M., Contreras-Martel, C., Blanot, D., Urleb, U., Dessen, A., Solmajer, T., Gobec, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.222 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 

Literature

Novel naphthalene-N-sulfonyl-D-glutamic acid derivatives as inhibitors of MurD, a key peptidoglycan biosynthesis enzyme.

Humljan, J., Kotnik, M., Contreras-Martel, C., Blanot, D., Urleb, U., Dessen, A., Solmajer, T., Gobec, S.

(2008) J Med Chem 51: 7486-7494

• PubMed: 19007109 
• DOI: 10.1021/jm800762u
• Primary Citation of Related Structures:  
  2VTD, 2VTE, 2UUO, 2UUP


• PubMed Abstract: 
  

Mur ligases have essential roles in the biosynthesis of peptidoglycan, and they represent attractive targets for the design of novel antibacterials. MurD (UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase) is the second enzyme in the series of Mur ligases, and it catalyzes the addition of D-glutamic acid (D-Glu) to the cytoplasmic intermediate UDP-N-acetylmuramoyl-L-alanine (UMA). Because of the high binding affinity of D-Glu toward MurD, we synthesized and biochemically evaluated a series of N-substituted D-Glu derivatives as potential inhibitors of MurD from E. coli, which allowed us to explore the structure-activity relationships.The substituted naphthalene-N-sulfonyl-D-Glu inhibitors, which were synthesized as potential transition state analogues, displayed IC50 values ranging from 80 to 600 microM. In addition, the high-resolution crystal structures of MurD in complex with four novel inhibitors revealed details of the binding mode of the inhibitors within the active site of MurD. Structure-activity relationships and cocrystal structures constitute an excellent starting point for further development of novel MurD inhibitors of this structural class.

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Organizational Affiliation: 

Drug Discovery, Lek Pharmaceuticals d.d., Verovskova 57, 1526 Ljubljana, Slovenia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE	A	445	Escherichia coli	Mutation(s): 0  EC: 6.3.2.9
Find proteins for P14900 (Escherichia coli (strain K12)) Explore P14900  Go to UniProtKB:  P14900

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LK4	A	N-({6-[(4-CYANOBENZYL)OXY]NAPHTHALEN-2-YL}SULFONYL)-D-GLUTAMIC ACID C23 H20 N2 O7 S PUHRQSFXADUGJW-OAQYLSRUSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
LK4	IC50:  105000   nM  Binding MOAD
LK4	IC50 :  105000   nM  PDBBind
LK4	IC50:  105000   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.222 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.517	α = 90
b = 65.517	β = 90
c = 136.174	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-03-06 
• Released Date: 2008-03-25 
Deposition Author(s): Humljan, J., Kotnik, M., Contreras-Martel, C., Blanot, D., Urleb, U., Dessen, A., Solmajer, T., Gobec, S.

Revision History 

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Database references, Source and taxonomy