Mtb InhA complex with Methyl-thiazole compound 7

Experimental Data Snapshot

  • Resolution: 1.89 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

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This is version 1.2 of the entry. See complete history


Methyl-Thiazoles: A Novel Mode of Inhibition with the Potential to Develop Novel Inhibitors Targeting Inha in Mycobacterium Tuberculosis.

Shirude, P.S.Madhavapeddi, P.Naik, M.Murugan, K.Shinde, V.Nandishaiah, R.Bhat, J.Kumar, A.Hameed, S.Holdgate, G.Davies, G.Mcmiken, H.Hegde, N.Ambady, A.Venkatraman, J.Panda, M.Bandodkar, B.Sambandamurthy, V.K.Read, J.A.

(2013) J Med Chem 56: 8533

  • DOI: https://doi.org/10.1021/jm4012033
  • Primary Citation of Related Structures:  
    4BQP, 4BQR

  • PubMed Abstract: 

    InhA is a well validated Mycobacterium tuberculosis (Mtb) target as evidenced by the clinical success of isoniazid. Translating enzyme inhibition to bacterial cidality by targeting the fatty acid substrate site of InhA remains a daunting challenge. The recent disclosure of a methyl-thiazole series demonstrates that bacterial cidality can be achieved with potent enzyme inhibition and appropriate physicochemical properties. In this study, we report the molecular mode of action of a lead methyl-thiazole, along with analogues with improved CYP inhibition profile. We have identified a novel mechanism of InhA inhibition characterized by a hitherto unreported "Y158-out" inhibitor-bound conformation of the protein that accommodates a neutrally charged "warhead". An additional novel hydrophilic interaction with protein residue M98 allows the incorporation of favorable physicochemical properties for cellular activity. Notably, the methyl-thiazole prefers the NADH-bound form of the enzyme with a Kd of ~13.7 nM, as against the NAD(+)-bound form of the enzyme.

  • Organizational Affiliation

    Department of Medicinal Chemistry, ‡Department of Biosciences, AstraZeneca India Pvt. Ltd. , Bellary Road, Hebbal, Bangalore-560024, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
269Mycobacterium tuberculosis H37RvMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
G [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
C21 H27 N7 O14 P2
Query on VMY

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F]
C18 H16 F2 N6 O S2
Query on NA

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
VMY BindingDB:  4BQP Kd: min: 12, max: 9300 (nM) from 3 assay(s)
IC50: min: 3, max: 4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.89 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.297α = 90
b = 81.304β = 95.25
c = 189.004γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-01-15
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other