8OTL | pdb_00008otl

structure of InhA from Mycobacterium tuberculosis in complex with 5-(((4-(2-hydroxyphenoxy)benzyl)(octyl)amino)methyl)-2-phenoxyphenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 
    0.237 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Exploring the plasticity of the InhA substrate-binding site using new diaryl ether inhibitors.

Tamhaev, R.Grosjean, E.Ahamed, H.Chebaiki, M.Rodriguez, F.Recchia, D.Degiacomi, G.Pasca, M.R.Maveyraud, L.Mourey, L.Lherbet, C.

(2023) Bioorg Chem 143: 107032-107032

  • DOI: https://doi.org/10.1016/j.bioorg.2023.107032
  • Primary Citation Related Structures: 
    8OTL

  • PubMed Abstract: 

    Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a worldwide scourge with more than 10 million people affected yearly. Among the proteins essential for the survival of Mtb, InhA has been and is still clinically validated as a therapeutic target. A new family of direct diaryl ether inhibitors, not requiring prior activation by the catalase peroxidase enzyme KatG, has been designed with the ambition of fully occupying the InhA substrate-binding site. Thus, eleven compounds, featuring three pharmacophores within the same molecule, were synthesized. One of them, 5-(((4-(2-hydroxyphenoxy)benzyl)(octyl)amino)methyl)-2-phenoxyphenol (compound 21), showed good inhibitory activity against InhA with IC 50 of 0.70 µM. The crystal structure of compound 21 in complex with InhA/NAD + showed how the molecule fills the substrate-binding site as well as the minor portal of InhA. This study represents a further step towards the design of new inhibitors of InhA.


  • Organizational Affiliation
    • Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (LSPCMIB), UMR 5068, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France.

Macromolecule Content 

  • Total Structure Weight: 177.77 kDa 
  • Atom Count: 12,589 
  • Modeled Residue Count: 1,598 
  • Deposited Residue Count: 1,632 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADH]
A, B, C, D, E
A, B, C, D, E, F
272Mycobacterium tuberculosisMutation(s): 0 
Gene Names: inhARv1484MTCY277.05
EC: 1.3.1.9
UniProt
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGR1 
Go to UniProtKB:  P9WGR1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGR1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
(Subject of Investigation/LOI)

Query on NAD



Download:Ideal Coordinates CCD File
G [auth A]
H [auth B]
I [auth C]
L [auth D]
N [auth E]
G [auth A],
H [auth B],
I [auth C],
L [auth D],
N [auth E],
P [auth F]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
VZE
(Subject of Investigation/LOI)

Query on VZE



Download:Ideal Coordinates CCD File
Q [auth F]5-[[octyl-[[4-(2-oxidanylphenoxy)phenyl]methyl]amino]methyl]-2-phenoxy-phenol
C34 H39 N O4
LSXDYGAOQCUIBL-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
K [auth C],
O [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
J [auth C],
M [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free:  0.237 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.85α = 90
b = 100.875β = 90
c = 376.071γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Universite de ToulouseFrance--
La Region OccitanieFrance--
Centre National de la Recherche Scientifique (CNRS)France--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release