5K4Z

M. thermoresistible IMPDH in complex with IMP and Compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Essential but Not Vulnerable: Indazole Sulfonamides Targeting Inosine Monophosphate Dehydrogenase as Potential Leads against Mycobacterium tuberculosis.

Park, Y.Pacitto, A.Bayliss, T.Cleghorn, L.A.Wang, Z.Hartman, T.Arora, K.Ioerger, T.R.Sacchettini, J.Rizzi, M.Donini, S.Blundell, T.L.Ascher, D.B.Rhee, K.Breda, A.Zhou, N.Dartois, V.Jonnala, S.R.Via, L.E.Mizrahi, V.Epemolu, O.Stojanovski, L.Simeons, F.Osuna-Cabello, M.Ellis, L.MacKenzie, C.J.Smith, A.R.Davis, S.H.Murugesan, D.Buchanan, K.I.Turner, P.A.Huggett, M.Zuccotto, F.Rebollo-Lopez, M.J.Lafuente-Monasterio, M.J.Sanz, O.Diaz, G.S.Lelievre, J.Ballell, L.Selenski, C.Axtman, M.Ghidelli-Disse, S.Pflaumer, H.Bosche, M.Drewes, G.Freiberg, G.M.Kurnick, M.D.Srikumaran, M.Kempf, D.J.Green, S.R.Ray, P.C.Read, K.Wyatt, P.Barry, C.E.Boshoff, H.I.

(2017) ACS Infect Dis 3: 18-33

  • DOI: 10.1021/acsinfecdis.6b00103
  • Primary Citation of Related Structures:  
    5K4X, 5K4Z

  • PubMed Abstract: 
  • A potent, noncytotoxic indazole sulfonamide was identified by high-throughput screening of >100,000 synthetic compounds for activity against Mycobacterium tuberculosis (Mtb). This noncytotoxic compound did not directly inhibit cell wall biogenesis but triggered a slow lysis of Mtb cells as measured by release of intracellular green fluorescent protein (GFP) ...

    A potent, noncytotoxic indazole sulfonamide was identified by high-throughput screening of >100,000 synthetic compounds for activity against Mycobacterium tuberculosis (Mtb). This noncytotoxic compound did not directly inhibit cell wall biogenesis but triggered a slow lysis of Mtb cells as measured by release of intracellular green fluorescent protein (GFP). Isolation of resistant mutants followed by whole-genome sequencing showed an unusual gene amplification of a 40 gene region spanning from Rv3371 to Rv3411c and in one case a potential promoter mutation upstream of guaB2 (Rv3411c) encoding inosine monophosphate dehydrogenase (IMPDH). Subsequent biochemical validation confirmed direct inhibition of IMPDH by an uncompetitive mode of inhibition, and growth inhibition could be rescued by supplementation with guanine, a bypass mechanism for the IMPDH pathway. Beads containing immobilized indazole sulfonamides specifically interacted with IMPDH in cell lysates. X-ray crystallography of the IMPDH-IMP-inhibitor complex revealed that the primary interactions of these compounds with IMPDH were direct pi-pi interactions with the IMP substrate. Advanced lead compounds in this series with acceptable pharmacokinetic properties failed to show efficacy in acute or chronic murine models of tuberculosis (TB). Time-kill experiments in vitro suggest that sustained exposure to drug concentrations above the minimum inhibitory concentration (MIC) for 24 h were required for a cidal effect, levels that have been difficult to achieve in vivo. Direct measurement of guanine levels in resected lung tissue from tuberculosis-infected animals and patients revealed 0.5-2 mM concentrations in caseum and normal lung tissue. The high lesional levels of guanine and the slow lytic, growth-rate-dependent effect of IMPDH inhibition pose challenges to developing drugs against this target for use in treating TB.


    Organizational Affiliation

    Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health , Bethesda, Maryland 20892-3206, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenaseA389Mycolicibacterium thermoresistibileMutation(s): 0 
Gene Names: RMCT_0580
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
6Q8 (Subject of Investigation/LOI)
Query on 6Q8

Download Ideal Coordinates CCD File 
C [auth A]~{N}-(4-fluorophenyl)-4-(2~{H}-indazol-6-ylsulfamoyl)-3,5-dimethyl-1~{H}-pyrrole-2-carboxamide
C20 H18 F N5 O3 S
LWWWROAXBQFQIU-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
6Q8 Binding MOAD:  5K4Z Kd: 700 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.27α = 90
b = 89.27β = 90
c = 84.76γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references