6R1O

Crystal structure of E. coli seryl-tRNA synthetase complexed to a seryl sulfamoyl adenosine derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-Guided Enhancement of Selectivity of Chemical Probe Inhibitors Targeting Bacterial Seryl-tRNA Synthetase.

Cain, R.Salimraj, R.Punekar, A.S.Bellini, D.Fishwick, C.W.G.Czaplewski, L.Scott, D.J.Harris, G.Dowson, C.G.Lloyd, A.J.Roper, D.I.

(2019) J Med Chem 62: 9703-9717

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01131
  • Primary Citation of Related Structures:  
    6R1M, 6R1N, 6R1O

  • PubMed Abstract: 

    Aminoacyl-tRNA synthetases are ubiquitous and essential enzymes for protein synthesis and also a variety of other metabolic processes, especially in bacterial species. Bacterial aminoacyl-tRNA synthetases represent attractive and validated targets for antimicrobial drug discovery if issues of prokaryotic versus eukaryotic selectivity and antibiotic resistance generation can be addressed. We have determined high-resolution X-ray crystal structures of the Escherichia coli and Staphylococcus aureus seryl-tRNA synthetases in complex with aminoacyl adenylate analogues and applied a structure-based drug discovery approach to explore and identify a series of small molecule inhibitors that selectively inhibit bacterial seryl-tRNA synthetases with greater than 2 orders of magnitude compared to their human homologue, demonstrating a route to the selective chemical inhibition of these bacterial targets.


  • Organizational Affiliation

    School of Life Sciences , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine--tRNA ligase437Escherichia coliMutation(s): 0 
Gene Names: serSECVG_02257
EC: 6.1.1.11
UniProt
Find proteins for P0A8L1 (Escherichia coli (strain K12))
Explore P0A8L1 
Go to UniProtKB:  P0A8L1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8L1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JPE (Subject of Investigation/LOI)
Query on JPE

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-pyridin-3-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate
C18 H22 N8 O8 S
AJLUWRJYNKUFKX-OBXKABKQSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
S [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS
Query on DMS

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
M [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.41α = 90
b = 85.41β = 90
c = 317.716γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/M017893/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Refinement description
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description