4QRE | pdb_00004qre

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

PDB DOI: https://doi.org/10.2210/pdb4QRE/pdb

Classification: LIGASE/LIGASE INHIBITOR
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.239 (Depositor), 0.232 (DCC)
R-Value Work:
0.202 (Depositor), 0.197 (DCC)
R-Value Observed:
0.204 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 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.

Macromolecule Content

Total Structure Weight: 64.19 kDa
Atom Count: 4,906
Modeled Residue Count: 519
Deposited Residue Count: 547
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionyl-tRNA synthetase	A	547	Staphylococcus aureus	Mutation(s): 0 Gene Names: metG, CH52_03385 EC: 6.1.1.10

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3BG Query on 3BG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth 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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.239 (Depositor), 0.232 (DCC)
R-Value Work: 0.202 (Depositor), 0.197 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.932	α = 90
b = 75.672	β = 90
c = 119.16	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-07-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-07-29
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.