4R9S

Mycobacterium tuberculosis InhA bound to NITD-916


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


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Literature

Direct inhibitors of InhA are active against Mycobacterium tuberculosis

Manjunatha, U.H.Rao, S.P.S.Kondreddi, R.R.Noble, C.G.Camacho, L.R.Tan, B.H.Ng, S.H.Ng, P.S.Ma, N.L.Lakshminarayana, S.B.Herve, M.Barnes, S.W.Yu, W.Kuhen, K.Blasco, F.Beer, D.Walker, J.R.Tonge, P.J.Glynne, R.Smith, P.W.Diagana, T.T.

(2015) Sci Transl Med 7: 269ra3-269ra3

  • DOI: 10.1126/scitranslmed.3010597
  • Primary Citation of Related Structures:  
    4R9R, 4R9S

  • PubMed Abstract: 
  • New chemotherapeutic agents are urgently required to combat the global spread of multidrug-resistant tuberculosis (MDR-TB). The mycobacterial enoyl reductase InhA is one of the few clinically validated targets in tuberculosis drug discovery. We report the identification of a new class of direct InhA inhibitors, the 4-hydroxy-2-pyridones, using phenotypic high-throughput whole-cell screening ...

    New chemotherapeutic agents are urgently required to combat the global spread of multidrug-resistant tuberculosis (MDR-TB). The mycobacterial enoyl reductase InhA is one of the few clinically validated targets in tuberculosis drug discovery. We report the identification of a new class of direct InhA inhibitors, the 4-hydroxy-2-pyridones, using phenotypic high-throughput whole-cell screening. This class of orally active compounds showed potent bactericidal activity against common isoniazid-resistant TB clinical isolates. Biophysical studies revealed that 4-hydroxy-2-pyridones bound specifically to InhA in an NADH (reduced form of nicotinamide adenine dinucleotide)-dependent manner and blocked the enoyl substrate-binding pocket. The lead compound NITD-916 directly blocked InhA in a dose-dependent manner and showed in vivo efficacy in acute and established mouse models of Mycobacterium tuberculosis infection. Collectively, our structural and biochemical data open up new avenues for rational structure-guided optimization of the 4-hydroxy-2-pyridone class of compounds for the treatment of MDR-TB.


    Organizational Affiliation

    Novartis Institute for Tropical Diseases, 138670 Singapore, Singapore. Yong Loo Lin School of Medicine, National University of Singapore, 119228 Singapore, Singapore. manjunatha.ujjini@novartis.com thierry.diagana@novartis.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADH]A,
B [auth C],
C [auth E],
D [auth G]
272Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: P425_01541RVBD_1484inhARv1484MTCY277.05
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A],
G [auth C],
I [auth E],
K [auth G]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
3KY
Query on 3KY

Download Ideal Coordinates CCD File 
F [auth A],
H [auth C],
J [auth E],
L [auth G]
6-[(4,4-dimethylcyclohexyl)methyl]-4-hydroxy-3-phenylpyridin-2(1H)-one
C20 H25 N O2
WKDRRKVUJLNFSR-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3KY BindingDB:  4R9S IC50: 570 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.579α = 90
b = 103.579β = 90
c = 121.391γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2015-01-21 
  • Deposition Author(s): Noble, C.G.

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release