4QRE

Structure of Methionyl-tRNA Synthetase in complex with 1-(4-{4-[(1H-benzimidazol-2-ylmethyl)amino]-6-(4,5-dimethoxy-2-methylphenoxy)pyrimidin-2-yl}piperazin-1-yl)ethanone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Discovery and SAR of a Novel Series of Pyrimidine Antibacterials Targeting Methionyl-tRNA Synthetase

Li, X.Hilgers, M.T.Stidham, M.Brown-Driver, V.Shaw, K.J.Finn, J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methionyl-tRNA synthetase A547Staphylococcus aureusMutation(s): 0 
Gene Names: metGCH52_03385
EC: 6.1.1.10
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3BG
Query on 3BG

Download Ideal Coordinates CCD File 
A
1-(4-{4-[(1H-benzimidazol-2-ylmethyl)amino]-6-(4,5-dimethoxy-2-methylphenoxy)pyrimidin-2-yl}piperazin-1-yl)ethanone
C27 H31 N7 O4
QDJWEGQUTGIBNS-UHFFFAOYSA-N
 Ligand Interaction
ATP
Query on ATP

Download Ideal Coordinates CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.932α = 90
b = 75.672β = 90
c = 119.16γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-06-30 
  • Released Date: 2015-07-29 
  • Deposition Author(s): Hilgers, M.T.

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release