6VUY

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT358


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

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This is version 1.2 of the entry. See complete history


Literature

Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis fromMycobacterium tuberculosis.

Punetha, A.Ngo, H.X.Holbrook, S.Y.L.Green, K.D.Willby, M.J.Bonnett, S.A.Krieger, K.Dennis, E.K.Posey, J.E.Parish, T.Tsodikov, O.V.Garneau-Tsodikova, S.

(2020) ACS Chem Biol 15: 1581-1594

  • DOI: https://doi.org/10.1021/acschembio.0c00184
  • Primary Citation of Related Structures:  
    6VUR, 6VUS, 6VUT, 6VUU, 6VUW, 6VUX, 6VUY, 6VUZ, 6VV0, 6VV1, 6VV2, 6VV3

  • PubMed Abstract: 

    The enhanced intracellular survival (Eis) protein of Mycobacterium tuberculosis ( Mtb ) is a versatile acetyltransferase that multiacetylates aminoglycoside antibiotics abolishing their binding to the bacterial ribosome. When overexpressed as a result of promoter mutations, Eis causes drug resistance. In an attempt to overcome the Eis-mediated kanamycin resistance of Mtb , we designed and optimized structurally unique thieno[2,3- d ]pyrimidine Eis inhibitors toward effective kanamycin adjuvant combination therapy. We obtained 12 crystal structures of enzyme-inhibitor complexes, which guided our rational structure-based design of 72 thieno[2,3- d ]pyrimidine analogues divided into three families. We evaluated the potency of these inhibitors in vitro as well as their ability to restore the activity of kanamycin in a resistant strain of Mtb , in which Eis was upregulated. Furthermore, we evaluated the metabolic stability of 11 compounds in vitro . This study showcases how structural information can guide Eis inhibitor design.


  • Organizational Affiliation

    Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetyltransferase Eis422Mycobacterium tuberculosis H37RvMutation(s): 1 
Gene Names: eisRv2416cMTCY253.04
EC: 2.3.1
UniProt
Find proteins for P9WFK7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFK7 
Go to UniProtKB:  P9WFK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFK7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RN4 (Subject of Investigation/LOI)
Query on RN4

Download Ideal Coordinates CCD File 
B [auth A](7S)-7-phenyl-2-{[3-(piperidin-1-yl)propyl]sulfanyl}-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-amine
C24 H30 N4 S2
IMHDFRLOCDDLHN-SFHVURJKSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG
Query on MG

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N [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
M [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.047α = 90
b = 175.047β = 90
c = 123.557γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI090048

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description