4OHU

Crystal structure of Mycobacterium tuberculosis InhA in complex with inhibitor PT92


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

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
  • Structures With Same Primary Citation

  • 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.


    Related Citations: 
    • Time-dependent diaryl ether inhibitors of InhA: SAR studies of enzyme inhibition, antibacterial activity, and in vivo efficacy
      Pan, P., Knudson, S., 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.
      () To be published --: --

    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, D289Mycobacterium tuberculosisMutation(s): 0 
Gene Names: inhARv1484MT1531MTCY277.05
EC: 1.3.1.9
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGR1 
Go to UniProtKB:  P9WGR1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
2TK
Query on 2TK

Download CCD File 
A, B, C, D
2-(2-bromophenoxy)-5-hexylphenol
C18 H21 Br O2
XMFJZZCTDKMLKQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2TKKi:  0.20000000298023224   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.845α = 90
b = 90.486β = 90
c = 161.825γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-30
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description