4OYR

Competition of the small inhibitor PT91 with large fatty acyl substrate of the Mycobacterium tuberculosis enoyl-ACP reductase InhA by induced substrate-binding loop refolding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2995 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Structural and Energetic Model for the Slow-Onset Inhibition of the Mycobacterium tuberculosis Enoyl-ACP Reductase InhA.

Li, H.J.Lai, C.T.Pan, P.Yu, W.Liu, N.Bommineni, G.R.Garcia-Diaz, M.Simmerling, C.Tonge, P.J.

(2014) Acs Chem.Biol. 9: 986-993

  • DOI: 10.1021/cb400896g
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Slow-onset enzyme inhibitors are of great interest for drug discovery programs since the slow dissociation of the inhibitor from the drug-target complex results in sustained target occupancy leading to improved pharmacodynamics. However, the structur ...

    Slow-onset enzyme inhibitors are of great interest for drug discovery programs since the slow dissociation of the inhibitor from the drug-target complex results in sustained target occupancy leading to improved pharmacodynamics. However, the structural basis for slow-onset inhibition is often not fully understood, hindering the development of structure-kinetic relationships and the rational optimization of drug-target residence time. Previously we demonstrated that slow-onset inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA correlated with motions of a substrate-binding loop (SBL) near the active site. In the present work, X-ray crystallography and molecular dynamics simulations have been used to map the structural and energetic changes of the SBL that occur upon enzyme inhibition. Helix-6 within the SBL adopts an open conformation when the inhibitor structure or binding kinetics is substrate-like. In contrast, slow-onset inhibition results in large-scale local refolding in which helix-6 adopts a closed conformation not normally populated during substrate turnover. The open and closed conformations of helix-6 are hypothesized to represent the EI and EI* states on the two-step induced-fit reaction coordinate for enzyme inhibition. These two states were used as the end points for nudged elastic band molecular dynamics simulations resulting in two-dimensional potential energy profiles that reveal the barrier between EI and EI*, thus rationalizing the binding kinetics observed with different inhibitors. Our findings indicate that the structural basis for slow-onset kinetics can be understood once the structures of both EI and EI* have been identified, thus providing a starting point for the rational control of enzyme-inhibitor binding kinetics.


    Organizational Affiliation

    Institute for Chemical Biology and Drug Discovery, ‡Laufer Center for Physical and Quantitative Biology and §Department of Chemistry, ∥Graduate Program in Biochemistry and Structural Biology, and ⊥Department of Pharmacological Sciences, Stony Brook University , Stony Brook, New York 11794, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Enoyl-[acyl-carrier-protein] reductase [NADH]
A, B, C, D
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
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
1US
Query on 1US

Download SDF File 
Download CCD File 
A, B, C, D
2-(2-chloranylphenoxy)-5-hexyl-phenol
C18 H21 Cl O2
QXCNLBOWURGQPC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1USKi: 0.96 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2995 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.842α = 90.00
b = 90.653β = 90.00
c = 164.436γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PHENIXrefinement
HKL-2000data collection
MOLREPphasing
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM102864
Department of Energy (United States)United States--
National Institutes of Health/National Center for Research ResourcesUnited StatesP41RR012408

Revision History 

  • Version 1.0: 2014-04-30
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Advisory, Author supporting evidence, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary