4YFN

Escherichia coli RNA polymerase in complex with squaramide compound 14 (N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.82 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

X-ray Crystal Structures of Escherichia coli RNA Polymerase with Switch Region Binding Inhibitors Enable Rational Design of Squaramides with an Improved Fraction Unbound to Human Plasma Protein.

Molodtsov, V.Fleming, P.R.Eyermann, C.J.Ferguson, A.D.Foulk, M.A.McKinney, D.C.Masse, C.E.Buurman, E.T.Murakami, K.S.

(2015) J Med Chem 58: 3156-3171

  • DOI: 10.1021/acs.jmedchem.5b00050
  • Primary Citation of Related Structures:  
    4YFX, 4YFK, 4YFN

  • PubMed Abstract: 
  • Squaramides constitute a novel class of RNA polymerase inhibitors of which genetic evidence and computational modeling previously have suggested an inhibitory mechanism mediated by binding to the RNA polymerase switch region. An iterative chemistry p ...

    Squaramides constitute a novel class of RNA polymerase inhibitors of which genetic evidence and computational modeling previously have suggested an inhibitory mechanism mediated by binding to the RNA polymerase switch region. An iterative chemistry program increased the fraction unbound to human plasma protein from below minimum detection levels, i.e., <1% to 4-6%, while retaining biochemical potency. Since in vitro antimicrobial activity against an efflux-negative strain of Haemophilus influenzae was 4- to 8-fold higher, the combined improvement was at least 20- to 60-fold. Cocrystal structures of Escherichia coli RNA polymerase with two key squaramides showed displacement of the switch 2, predicted to interfere with the conformational change of the clamp domain and/or with binding of template DNA, a mechanism akin to that of natural product myxopyronin. Furthermore, the structures confirmed the chemical features required for biochemical potency. The terminal isoxazole and benzyl rings bind into distinct relatively narrow, hydrophobic pockets, and both are required for biochemical potency. In contrast, the linker composed of squarate and piperidine accesses different conformations in their respective cocrystal structures with RNA polymerase, reflecting its main role of proper orientation of the aforementioned terminal rings. These observations further explain the tolerance of hydrophilic substitutions in the linker region that was exploited to improve the fraction unbound to human plasma protein while retaining biochemical potency.


    Organizational Affiliation

    †Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaABGH329Escherichia coli O139:H28 str. E24377AMutation(s): 0 
Gene Names: rpoAEcE24377A_3778
EC: 2.7.7.6
Find proteins for A7ZSI4 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Explore A7ZSI4 
Go to UniProtKB:  A7ZSI4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaCI1342Escherichia coli O139:H28 str. E24377AMutation(s): 0 
Gene Names: rpoBEcE24377A_4528
EC: 2.7.7.6
Find proteins for A7ZUK1 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Explore A7ZUK1 
Go to UniProtKB:  A7ZUK1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'DJ1407Escherichia coli O139:H28 str. E24377AMutation(s): 0 
Gene Names: rpoCEcE24377A_4529
EC: 2.7.7.6
Find proteins for A7ZUK2 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Explore A7ZUK2 
Go to UniProtKB:  A7ZUK2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaEK91Escherichia coli O139:H28 str. E24377AMutation(s): 0 
Gene Names: rpoZEcE24377A_4152
EC: 2.7.7.6
Find proteins for A7ZTK1 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Explore A7ZTK1 
Go to UniProtKB:  A7ZTK1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDFL613Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoDaltb3067JW3039
Find proteins for P00579 (Escherichia coli (strain K12))
Explore P00579 
Go to UniProtKB:  P00579
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4C2
Query on 4C2

Download Ideal Coordinates CCD File 
D, J
N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide
C22 H23 F3 N4 O5 S
WFHJESWCVOQIPR-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D, J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.82 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.247α = 90
b = 206.569β = 90
c = 312.146γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM087350

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-04-08
    Changes: Database references
  • Version 1.2: 2015-04-22
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence