6GK9

Inhibited structure of IMPDH from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

First-in-class allosteric inhibitors of bacterial IMPDHs.

Alexandre, T.Lupan, A.Helynck, O.Vichier-Guerre, S.Dugue, L.Gelin, M.Haouz, A.Labesse, G.Munier-Lehmann, H.

(2019) Eur J Med Chem 167: 124-132

  • DOI: https://doi.org/10.1016/j.ejmech.2019.01.064
  • Primary Citation of Related Structures:  
    6GJV, 6GK9

  • PubMed Abstract: 

    Inosine-5'-monophosphate dehydrogenase (IMPDH) is an essential enzyme in many bacterial pathogens and is considered as a potential drug target for the development of new antibacterial agents. Our recent work has revealed the crucial role of one of the two structural domains (i.e. Bateman domain) in the regulation of the quaternary structure and enzymatic activity of bacterial IMPDHs. Thus, we have screened chemical libraries to search for compounds targeting the Bateman domain and identified first in-class allosteric inhibitors of a bacterial IMPDH. These inhibitors were shown to counteract the activation by the natural positive effector, MgATP, and to block the enzyme in its apo conformation (low affinity for IMP). Our structural studies demonstrate the versatility of the Bateman domain to accommodate totally unrelated chemical scaffolds and pave the way for the development of allosteric inhibitors, an avenue little explored until now.


  • Organizational Affiliation

    Institut Pasteur, Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, CNRS UMR3523, 28 rue du Dr Roux, F-75015, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, F-75205, Paris, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H
509Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: guaBPA3770
EC: 1.1.1.205
UniProt
Find proteins for Q9HXM5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HXM5 
Go to UniProtKB:  Q9HXM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HXM5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F2K
Query on F2K

Download Ideal Coordinates CCD File 
I [auth A],
J [auth D]
(5~{S})-7-azanyl-5-(4-chlorophenyl)-2,4-bis(oxidanylidene)-1,5-dihydropyrano[2,3-d]pyrimidine-6-carbonitrile
C14 H9 Cl N4 O3
BQFPJAOKBASIPO-VIFPVBQESA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth E]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.64α = 90
b = 196.958β = 113.99
c = 123.628γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Advisory, Data collection, Database references, Refinement description