7OR2

Crystal structure of UDP-N-acetylenolpyruvoylglucosamine reductase (MurB) from Pseudomonas aeruginosa in complex with FAD and a pyrazole derivative (fragment 4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Discovery of Novel Inhibitors of Uridine Diphosphate- N -Acetylenolpyruvylglucosamine Reductase (MurB) from Pseudomonas aeruginosa , an Opportunistic Infectious Agent Causing Death in Cystic Fibrosis Patients.

Acebron-Garcia-de-Eulate, M.Mayol-Llinas, J.Holland, M.T.O.Kim, S.Y.Brown, K.P.Marchetti, C.Hess, J.Di Pietro, O.Mendes, V.Abell, C.Floto, R.A.Coyne, A.G.Blundell, T.L.

(2022) J Med Chem 65: 2149-2173

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01684
  • Primary Citation of Related Structures:  
    7OR2, 7ORZ, 7OSQ

  • PubMed Abstract: 

    Pseudomonas aeruginosa is of major concern for cystic fibrosis patients where this infection can be fatal. With the emergence of drug-resistant strains, there is an urgent need to develop novel antibiotics against P. aeruginosa . MurB is a promising target for novel antibiotic development as it is involved in the cell wall biosynthesis. MurB has been shown to be essential in P. aeruginosa , and importantly, no MurB homologue exists in eukaryotic cells. A fragment-based drug discovery approach was used to target Pa MurB. This led to the identification of a number of fragments, which were shown to bind to MurB. One fragment, a phenylpyrazole scaffold, was shown by ITC to bind with an affinity of K d = 2.88 mM (LE 0.23). Using a structure guided approach, different substitutions were synthesized and the initial fragment was optimized to obtain a small molecule with K d = 3.57 μM (LE 0.35).


  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylenolpyruvoylglucosamine reductase340Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: murBPA2977
EC: 1.3.1.98
UniProt
Find proteins for Q9HZM7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HZM7 
Go to UniProtKB:  Q9HZM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HZM7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
9FH (Subject of Investigation/LOI)
Query on 9FH

Download Ideal Coordinates CCD File 
C [auth A]5-methyl-1-phenyl-pyrazole-4-carboxylic acid
C11 H10 N2 O2
USSMIQWDLWJQDQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.22α = 90
b = 87.22β = 90
c = 101.39γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited KingdomCystic Fibrosis Trust

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Data collection, Database references
  • Version 1.2: 2022-02-23
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description