5UGU

Crystal structure of M. tuberculosis InhA inhibited by PT506


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evaluating the Contribution of Transition-State Destabilization to Changes in the Residence Time of Triazole-Based InhA Inhibitors.

Spagnuolo, L.A.Eltschkner, S.Yu, W.Daryaee, F.Davoodi, S.Knudson, S.E.Allen, E.K.Merino, J.Pschibul, A.Moree, B.Thivalapill, N.Truglio, J.J.Salafsky, J.Slayden, R.A.Kisker, C.Tonge, P.J.

(2017) J. Am. Chem. Soc. 139: 3417-3429

  • DOI: 10.1021/jacs.6b11148
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A critical goal of lead compound selection and optimization is to maximize target engagement while minimizing off-target binding. Since target engagement is a function of both the thermodynamics and kinetics of drug-target interactions, it follows th ...

    A critical goal of lead compound selection and optimization is to maximize target engagement while minimizing off-target binding. Since target engagement is a function of both the thermodynamics and kinetics of drug-target interactions, it follows that the structures of both the ground states and transition states on the binding reaction coordinate are needed to rationally modulate the lifetime of the drug-target complex. Previously, we predicted the structure of the rate-limiting transition state that controlled the time-dependent inhibition of the enoyl-ACP reductase InhA. This led to the discovery of a triazole-containing diphenyl ether with an increased residence time on InhA due to transition-state destabilization rather than ground-state stabilization. In the present work, we evaluate the inhibition of InhA by 14 triazole-based diphenyl ethers and use a combination of enzyme kinetics and X-ray crystallography to generate a structure-kinetic relationship for time-dependent binding. We show that the triazole motif slows the rate of formation for the final drug-target complex by up to 3 orders of magnitude. In addition, we identify a novel inhibitor with a residence time on InhA of 220 min, which is 3.5-fold longer than that of the INH-NAD adduct formed by the tuberculosis drug, isoniazid. This study provides a clear example in which the lifetime of the drug-target complex is controlled by interactions in the transition state for inhibitor binding rather than the ground state of the enzyme-inhibitor complex, and demonstrates the important role that on-rates can play in drug-target residence time.


    Organizational Affiliation

    Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States.




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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XTV
Query on XTV

Download SDF File 
Download CCD File 
A
2-[4-[(4-cyclopropyl-1,2,3-triazol-1-yl)methyl]-2-oxidanyl-phenoxy]benzenecarbonitrile
C19 H16 N4 O2
LHTWMYAWMSNPIN-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.164 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 90.655α = 90.00
b = 90.655β = 90.00
c = 182.880γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
XDSdata reduction
REFMACrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB 630

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence