7RWI

Mycobacterium tuberculosis RNA polymerase sigma L holoenzyme open promoter complex containing TNP-2198


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design, Synthesis, and Characterization of TNP-2198, a Dual-Targeted Rifamycin-Nitroimidazole Conjugate with Potent Activity against Microaerophilic and Anaerobic Bacterial Pathogens.

Ma, Z.He, S.Yuan, Y.Zhuang, Z.Liu, Y.Wang, H.Chen, J.Xu, X.Ding, C.Molodtsov, V.Lin, W.Robertson, G.T.Weiss, W.J.Pulse, M.Nguyen, P.Duncan, L.Doyle, T.Ebright, R.H.Lynch, A.S.

(2022) J Med Chem 65: 4481-4495

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c02045
  • Primary Citation of Related Structures:  
    7RWI

  • PubMed Abstract: 

    TNP-2198, a stable conjugate of a rifamycin pharmacophore and a nitroimidazole pharmacophore, has been designed, synthesized, and evaluated as a novel dual-targeted antibacterial agent for the treatment of microaerophilic and anaerobic bacterial infections. TNP-2198 exhibits greater activity than a 1:1 molar mixture of the parent drugs and exhibits activity against strains resistant to both rifamycins and nitroimidazoles. A crystal structure of TNP-2198 bound to a Mycobacterium tuberculosis RNA polymerase transcription initiation complex reveals that the rifamycin portion of TNP-2198 binds to the rifamycin binding site on RNAP and the nitroimidazole portion of TNP-2198 interacts directly with the DNA template-strand in the RNAP active-center cleft, forming a hydrogen bond with a base of the DNA template strand. TNP-2198 is currently in Phase 2 clinical development for the treatment of Helicobacter pylori infection, Clostridioides difficile infection, and bacterial vaginosis.


  • Organizational Affiliation

    TenNor Therapeutics Ltd, 218 Xinghu Street, Suzhou Industrial Park, Suzhou 215123, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
347Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
UniProt
Find proteins for P9WGZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Go to UniProtKB:  P9WGZ1
Entity Groups  
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UniProt GroupP9WGZ1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,178Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
UniProt
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Go to UniProtKB:  P9WGY9
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UniProt GroupP9WGY9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,316Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 2.7.7.6
UniProt
Find proteins for P9WGY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WGY7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega110Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 2.7.7.6
UniProt
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WGY5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor177Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P9WGH5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WGH5
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  • Reference Sequence

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Entity ID: 6
MoleculeChains LengthOrganismImage
T DNA23synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
NT DNA27synthetic construct
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7US
Query on 7US

Download Ideal Coordinates CCD File 
I [auth C](3aM,9S,10bP,14S,15R,16S,17R,18R,19R,20S,21S,25R)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate
C48 H67 N7 O13
YCJZZHMRIASIJJ-XTGRINFNSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.773α = 90
b = 160.613β = 90
c = 238.646γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description