4XWA | pdb_00004xwa

TMK from S.aureus in complex with the Piperidinyl Thymine class inhibitor with a C5 ethyl-amine

PDB DOI: https://doi.org/10.2210/pdb4XWA/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus Mu3
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2015-01-28 Released: 2015-02-11
Deposition Author(s): Olivier, N.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.229 (Depositor), 0.230 (DCC)
R-Value Work:
0.193 (Depositor), 0.190 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A highly potent antibacterial inhibitor of Gram-positive bacterial thymidylate kinase (TMK): SAR of piperidinyl thymines at position C5 and L1

Guler, S.Y., Martinez-Botella, G., Breen, J., Kawatkar, S., Loch, J., Olivier, N.B., Wang, H., Keating, T., Otterson, L.

(2015) Bioorg Med Chem Lett

Macromolecule Content

Total Structure Weight: 48.09 kDa
Atom Count: 3,529
Modeled Residue Count: 398
Deposited Residue Count: 410
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate kinase	A, B	205	Staphylococcus aureus subsp. aureus Mu3	Mutation(s): 0 Gene Names: tmk, SAHV_0479 EC: 2.7.4.9
UniProt
Find proteins for A7WYM2 (Staphylococcus aureus (strain Mu3 / ATCC 700698)) Explore A7WYM2 Go to UniProtKB: A7WYM2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7WYM2
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
43N Query on 43N Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	2-(3-chlorophenoxy)-6-(ethylamino)-4-[(R)-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl](phenyl)methyl]benzoic acid C₃₂ H₃₃ Cl N₄ O₅ XESNVVRXJFEIMM-PWUYWRBVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.229 (Depositor), 0.230 (DCC)
R-Value Work: 0.193 (Depositor), 0.190 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.483	α = 90
b = 89.806	β = 99.29
c = 50.875	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
AMoRE	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-02-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-02-11
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Database references, Refinement description

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.