7OSQ | pdb_00007osq

Crystal structure of UDP-N-acetylenolpyruvoylglucosamine reductase (MurB) from Pseudomonas aeruginosa in complex with FAD and a pyrazole derivative (fragment 18)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 
    0.252 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7OSQ

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 38.67 kDa 
  • Atom Count: 2,679 
  • Modeled Residue Count: 337 
  • Deposited Residue Count: 339 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UDP-N-acetylenolpyruvoylglucosamine reductase339Pseudomonas 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
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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
0JI
(Subject of Investigation/LOI)

Query on 0JI



Download:Ideal Coordinates CCD File
C [auth A]5-methyl-1-phenyl-1,2,3-triazole-4-carboxylic acid
C10 H9 N3 O2
RRHCZOBPABYIJZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free:  0.252 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.651α = 90
b = 87.651β = 90
c = 101.148γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
PHASERphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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