4QRD | pdb_00004qrd

Structure of Methionyl-tRNA Synthetase in complex with N-(1H-benzimidazol-2-ylmethyl)-N'-(2,4-dichlorophenyl)-6-(morpholin-4-yl)-1,3,5-triazine-2,4-diamine

PDB DOI: https://doi.org/10.2210/pdb4QRD/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): Li, X., Hilgers, M.T., Stidham, M., Brown-Driver, V., Shaw, K.J., Finn, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.283 (Depositor), 0.280 (DCC)
R-Value Work:
0.201 (Depositor), 0.210 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

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: 63.61 kDa
Atom Count: 4,520
Modeled Residue Count: 519
Deposited Residue Count: 547
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3BJ Query on 3BJ 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]	N-(1H-benzimidazol-2-ylmethyl)-N'-(2,4-dichlorophenyl)-6-(morpholin-4-yl)-1,3,5-triazine-2,4-diamine C₂₁ H₂₀ Cl₂ N₈ O PFJXETPWVKVWSZ-UHFFFAOYSA-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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.283 (Depositor), 0.280 (DCC)
R-Value Work: 0.201 (Depositor), 0.210 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.438	α = 90
b = 76.726	β = 90
c = 118.222	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
MOSFLM	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-07-29

Deposition Author(s):

Brown-Driver, V.

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

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.