6R1M

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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Ligand Structure Quality Assessment 


This is version 1.0 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Serine--tRNA ligaseA, B437Escherichia 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SSA (Subject of Investigation/LOI)
Query on SSA

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
C13 H19 N7 O8 S
HQXFJGONGJPTLZ-YTMOPEAISA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A],
O [auth B],
P [auth B],
Q [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SSA BindingDB:  6R1M Ki: 0.18 (nM) from 1 assay(s)
Kd: 1.3 (nM) from 1 assay(s)
IC50: 210 (nM) from 1 assay(s)
Binding MOAD:  6R1M IC50: 210 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.07α = 75.44
b = 63.52β = 70.25
c = 75.89γ = 89.2
Software Package:
Software NamePurpose
BUSTERrefinement
iMOSFLMdata reduction
Aimlessdata 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