4OIM

Crystal structure of Mycobacterium tuberculosis InhA in complex with inhibitor PT119 in 2.4 M acetate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.848 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Time-Dependent Diaryl Ether Inhibitors of InhA: Structure-Activity Relationship Studies of Enzyme Inhibition, Antibacterial Activity, and in vivo Efficacy.

Pan, P.Knudson, S.E.Bommineni, G.R.Li, H.J.Lai, C.T.Liu, N.Garcia-Diaz, M.Simmerling, C.Patil, S.S.Slayden, R.A.Tonge, P.J.

(2014) Chemmedchem 9: 776-791

  • DOI: 10.1002/cmdc.201300429

  • PubMed Abstract: 
  • The diaryl ethers are a novel class of antituberculosis drug candidates that inhibit InhA, the enoyl-ACP reductase involved in the fatty acid biosynthesis (FASII) pathway, and have antibacterial activity against both drug-sensitive and drug-resistant ...

    The diaryl ethers are a novel class of antituberculosis drug candidates that inhibit InhA, the enoyl-ACP reductase involved in the fatty acid biosynthesis (FASII) pathway, and have antibacterial activity against both drug-sensitive and drug-resistant strains of Mycobacterium tuberculosis. In the present work, we demonstrate that two time-dependent B-ring modified diaryl ether InhA inhibitors have antibacterial activity in a mouse model of TB infection when delivered by intraperitoneal injection. We propose that the efficacy of these compounds is related to their residence time on the enzyme, and to identify structural features that modulate drug-target residence time in this system, we have explored the inhibition of InhA by a series of B-ring modified analogues. Seven ortho-substituted compounds were found to be time-dependent inhibitors of InhA, where the slow step leading to the final enzyme-inhibitor complex (EI*) is thought to correlate with closure and ordering of the InhA substrate binding loop. A detailed mechanistic understanding of the molecular basis for residence time in this system will facilitate the development of InhA inhibitors with improved in vivo activity.


    Related Citations: 
    • A Structural and energetic model for the slow-onset inhibition of InhA, an enzyme drug target from Mycobacterium tuberculosis
      Li, H.J.,Lai, C.T.,Pan, P.,Yu, W.,Liu, N.,Garcia-Diaz, M.,Simmerling, C.,Tonge, P.J.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400 (USA).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Enoyl-[acyl-carrier-protein] reductase [NADH]
A
289Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: inhA
EC: 1.3.1.9
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGR1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
JUS
Query on JUS

Download SDF File 
Download CCD File 
A
2-(2-CYANOPHENOXY)-5-HEXYLPHENOL
C19 H21 N O2
RPZKERMNVCALKE-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JUSKi: 2.14 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.848 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 90.622α = 90.00
b = 90.622β = 90.00
c = 182.634γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
PHENIXrefinement
SCALEPACKdata scaling
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description