5HS3

Human thymidylate synthase complexed with dUMP and 3-amino-2-benzoyl-4-methylthieno[2,3-b]pyridin-6-ol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.103 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

CETSA screening identifies known and novel thymidylate synthase inhibitors and slow intracellular activation of 5-fluorouracil

Almqvist, H.Axelsson, H.Jafari, R.Chen, D.Mateus, A.Haraldsson, M.Larsson, A.Molina, D.M.Artursson, P.Lundback, T.Nordlund, P.

(2016) Nat Commun 7: 11040-11040

  • DOI: 10.1038/ncomms11040

  • PubMed Abstract: 
  • Target engagement is a critical factor for therapeutic efficacy. Assessment of compound binding to native target proteins in live cells is therefore highly desirable in all stages of drug discovery. We report here the first compound library screen ba ...

    Target engagement is a critical factor for therapeutic efficacy. Assessment of compound binding to native target proteins in live cells is therefore highly desirable in all stages of drug discovery. We report here the first compound library screen based on biophysical measurements of intracellular target binding, exemplified by human thymidylate synthase (TS). The screen selected accurately for all the tested known drugs acting on TS. We also identified TS inhibitors with novel chemistry and marketed drugs that were not previously known to target TS, including the DNA methyltransferase inhibitor decitabine. By following the cellular uptake and enzymatic conversion of known drugs we correlated the appearance of active metabolites over time with intracellular target engagement. These data distinguished a much slower activation of 5-fluorouracil when compared with nucleoside-based drugs. The approach establishes efficient means to associate drug uptake and activation with target binding during drug discovery.


    Organizational Affiliation

    Department of Medical Biochemistry &Biophysics, Division of Biophysics, Karolinska Institutet, Scheeles väg 2, Stockholm 171 77, Sweden.,Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Uppsala University, BMC, Box 580, Uppsala SE-751 23, Sweden.,School of Biological Sciences, Nanyang Technological University, 61 Biopolis Drive (Proteos), Singapore 138673, Singapore.,Department of Pharmacy, Uppsala University, BMC, Box 580, Uppsala SE-751 23, Sweden.,Institute of Cellular and Molecular Biology, ASTAR, 61 Biopolis Drive (Proteos), Singapore 138673, Singapore.,Laboratories for Chemical Biology, Karolinska Institutet, Science for Life Laboratory Stockholm, Division of Translational Medicine &Chemical Biology, Department of Medical Biochemistry &Biophysics, Karolinska Institutet, Tomtebodavägen 23A, Solna 171 65, Sweden.,School of Biological Sciences, Nanyang Technological University, SBS-04s-45, 60 Nanyang Drive, Singapore 639798, Singapore.,Science for Life Laboratory Drug Discovery and Development platform, Uppsala University, Uppsala SE-751 23, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase
A, B, C, D, E, F
289Homo sapiensMutation(s): 0 
Gene Names: TYMS (TS)
EC: 2.1.1.45
Find proteins for P04818 (Homo sapiens)
Go to Gene View: TYMS
Go to UniProtKB:  P04818
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KI3
Query on KI3

Download SDF File 
Download CCD File 
A, B, E
3-amino-2-benzoyl-4-methylthieno[2,3-b]pyridin-6-ol
C15 H12 N2 O2 S
PNCPOBGZUHFDDF-UHFFFAOYSA-N
 Ligand Interaction
UMP
Query on UMP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.103 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.180 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 108.202α = 90.00
b = 108.202β = 90.00
c = 313.931γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Nanyang Technological UniversitySingaporeM060080004.70301200

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references
  • Version 1.2: 2016-04-06
    Type: Database references