7U22

Mycobacterium tuberculosis RNA polymerase sigma A holoenzyme open promoter complex containing UMN-7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.87 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Redesign of Rifamycin Antibiotics to Overcome ADP-Ribosylation-Mediated Resistance.

Lan, T.Ganapathy, U.S.Sharma, S.Ahn, Y.M.Zimmerman, M.Molodtsov, V.Hegde, P.Gengenbacher, M.Ebright, R.H.Dartois, V.Freundlich, J.S.Dick, T.Aldrich, C.C.

(2022) Angew Chem Int Ed Engl 61: e202211498-e202211498

  • DOI: https://doi.org/10.1002/anie.202211498
  • Primary Citation of Related Structures:  
    7U22

  • PubMed Abstract: 

    Rifamycin antibiotics are a valuable class of antimicrobials for treating infections by mycobacteria and other persistent bacteria owing to their potent bactericidal activity against replicating and non-replicating pathogens. However, the clinical utility of rifamycins against Mycobacterium abscessus is seriously compromised by a novel resistance mechanism, namely, rifamycin inactivation by ADP-ribosylation. Using a structure-based approach, we rationally redesign rifamycins through strategic modification of the ansa-chain to block ADP-ribosylation while preserving on-target activity. Validated by a combination of biochemical, structural, and microbiological studies, the most potent analogs overcome ADP-ribosylation, restored their intrinsic low nanomolar activity and demonstrated significant in vivo antibacterial efficacy. Further optimization by tuning drug disposition properties afforded a preclinical candidate with remarkable potency and an outstanding pharmacokinetic profile.


  • Organizational Affiliation

    Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 308 SE Harvard St SE, Minneapolis, MN 55455, USA.


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))
Explore P9WGZ1 
Go to UniProtKB:  P9WGZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGZ1
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  • Reference Sequence
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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))
Explore P9WGY9 
Go to UniProtKB:  P9WGY9
Entity Groups  
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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))
Explore P9WGY7 
Go to UniProtKB:  P9WGY7
Entity Groups  
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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))
Explore P9WGY5 
Go to UniProtKB:  P9WGY5
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UniProt GroupP9WGY5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigA528Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P9WGI1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGI1 
Go to UniProtKB:  P9WGI1
Entity Groups  
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UniProt GroupP9WGI1
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  • Reference Sequence

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Entity ID: 6
MoleculeChains LengthOrganismImage
T DNA16Mycobacterium tuberculosis
Sequence Annotations
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Entity ID: 7
MoleculeChains LengthOrganismImage
NT DNA23Mycobacterium tuberculosis
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KYO (Subject of Investigation/LOI)
Query on KYO

Download Ideal Coordinates CCD File 
I [auth C](9S,14S,15R,16S,17R,18R,19R,20S,21S,25R)-5,6,18,20-tetrahydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-(2-methylpropyl)-10,26-dioxo-1,3,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl benzoate
C51 H72 N4 O11
MCRVPMWRSBLOPF-ZGLABKAESA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
J [auth D],
K [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
L [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.87 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.482α = 90
b = 161.445β = 90
c = 196.603γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-3000data reduction
SCALEPACKdata 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: 2022-10-19
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description