6D4S

M. thermoresistible GuaB2 delta-CBS in complex with inhibitor Compound 37 (VCC670597)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Synthesis and Structure-Activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH.

Singh, V.Pacitto, A.Donini, S.Ferraris, D.M.Boros, S.Illyes, E.Szokol, B.Rizzi, M.Blundell, T.L.Ascher, D.B.Pato, J.Mizrahi, V.

(2019) Eur J Med Chem 174: 309-329

  • DOI: 10.1016/j.ejmech.2019.04.027
  • Primary Citation of Related Structures:  
    6D4W, 6D4V, 6D4Q, 6D4S, 6D4R, 6D4U, 6D4T

  • PubMed Abstract: 
  • Tuberculosis (TB) is a major infectious disease associated increasingly with drug resistance. Thus, new anti-tubercular agents with novel mechanisms of action are urgently required for the treatment of drug-resistant TB. In prior work, we identified compound 1 (cyclohexyl(4-(isoquinolin-5-ylsulfonyl)piperazin-1-yl)methanone) and showed that its anti-tubercular activity is attributable to inhibition of inosine-5'-monophosphate dehydrogenase (IMPDH) in Mycobacterium tuberculosis ...

    Tuberculosis (TB) is a major infectious disease associated increasingly with drug resistance. Thus, new anti-tubercular agents with novel mechanisms of action are urgently required for the treatment of drug-resistant TB. In prior work, we identified compound 1 (cyclohexyl(4-(isoquinolin-5-ylsulfonyl)piperazin-1-yl)methanone) and showed that its anti-tubercular activity is attributable to inhibition of inosine-5'-monophosphate dehydrogenase (IMPDH) in Mycobacterium tuberculosis. In the present study, we explored the structure-activity relationship around compound 1 by synthesizing and evaluating the inhibitory activity of analogues against M. tuberculosis IMPDH in biochemical and whole-cell assays. X-ray crystallography was performed to elucidate the mode of binding of selected analogues to IMPDH. We establish the importance of the cyclohexyl, piperazine and isoquinoline rings for activity, and report the identification of an analogue with IMPDH-selective activity against a mutant of M. tuberculosis that is highly resistant to compound 1. We also show that the nitrogen in urea analogues is required for anti-tubercular activity and identify benzylurea derivatives as promising inhibitors that warrant further investigation.


    Organizational Affiliation

    MRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research & Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Anzio Road, Observatory, 7925, South Africa. Electronic address: valerie.mizrahi@uct.ac.za.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenaseA389Mycolicibacterium thermoresistibile ATCC 19527Mutation(s): 0 
Gene Names: guaBKEK_23061
EC: 1.1.1.205
UniProt
Find proteins for G7CNL4 (Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316))
Explore G7CNL4 
Go to UniProtKB:  G7CNL4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FWV (Subject of Investigation/LOI)
Query on FWV

Download Ideal Coordinates CCD File 
C [auth A]N-(2,3-dichlorophenyl)-4-[(isoquinolin-5-yl)sulfonyl]piperazine-1-carboxamide
C20 H18 Cl2 N4 O3 S
OPIJBEYHDBKGKX-UHFFFAOYSA-N
 Ligand Interaction
IMP (Subject of Investigation/LOI)
Query on IMP

Download Ideal Coordinates CCD File 
B [auth A]INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FWV Binding MOAD:  6D4S IC50: 900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.4α = 90
b = 89.4β = 90
c = 85.31γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European Union260872
Medical Research Council (MRC, United Kingdom)United KingdomMR/M026302/1
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1072476

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence