4XWA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report



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 


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate kinaseA, B205Staphylococcus aureus subsp. aureus Mu3Mutation(s): 0 
Gene Names: tmkSAHV_0479
EC: 2.7.4.9
Find proteins for A7WYM2 (Staphylococcus aureus (strain Mu3 / ATCC 700698))
Explore A7WYM2 
Go to UniProtKB:  A7WYM2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
43N
Query on 43N

Download CCD File 
A, 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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.483α = 90
b = 89.806β = 99.29
c = 50.875γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
AMoREphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2015-02-11
    Type: Initial release