4YFX

Escherichia coli RNA polymerase in complex with Myxopyronin B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.844 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  
  • Also Cited By: 4YG2

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B, G, H
329Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for A7ZSI4 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZSI4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C, I
1342Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for A7ZUK1 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZUK1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D, J
1407Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for A7ZUK2 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZUK2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E, K
91Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for A7ZTK1 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZTK1
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor RpoD
F, L
613Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoD (alt)
Find proteins for P00579 (Escherichia coli (strain K12))
Go to UniProtKB:  P00579
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D, J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
4C4
Query on 4C4

Download SDF File 
Download CCD File 
D
Myxopyronin B
C24 H33 N O6
SPQDIDVJAZFBRL-WXFBSNOUSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.844 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 188.520α = 90.00
b = 205.177β = 90.00
c = 310.140γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-04-08
    Type: Database references, Non-polymer description
  • Version 1.2: 2015-04-22
    Type: Database references