4E28

Structure of human thymidylate synthase in inactive conformation with a novel non-peptidic inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4E28/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-07 Released: 2012-11-14 
• Deposition Author(s): Tochowicz, A., Finer-Moore, J., Stroud, R.M., Costi, M.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.229 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Inhibitor of ovarian cancer cells growth by virtual screening: a new thiazole derivative targeting human thymidylate synthase.

Carosati, E., Tochowicz, A., Marverti, G., Guaitoli, G., Benedetti, P., Ferrari, S., Stroud, R.M., Finer-Moore, J., Luciani, R., Farina, D., Cruciani, G., Costi, M.P.

(2012) J Med Chem 55: 10272-10276

• PubMed: 23075414 
• DOI: https://doi.org/10.1021/jm300850v
• Primary Citation of Related Structures:  
  4E28


• PubMed Abstract: 
  

  Human thymidylate synthase (hTS) was targeted through a virtual screening approach. The most optimal inhibitor identified, 2-{4-hydroxy-2-[(2-hydroxybenzylidene)hydrazono]-2,5-dihydrothiazol-5-yl}-N-(3-trifluoromethylphenyl)acetamide (5), showed a mixed-type inhibition pattern, with a K(i) of 1.3 μM and activity against ovarian cancer cell lines with the same potency as cisplatin. X-ray studies revealed that it binds the inactive enzyme conformation. This study is the first example of a nonpeptidic inhibitor that binds the inactive hTS and exhibits anticancer activity against ovarian cancer cells.

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Organizational Affiliation: 

Dipartimento di Chimica, Università degli Studi di Perugia , Via Elce di Sotto 10, 06123, Perugia, Italy.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.39 kDa 
• Atom Count: 2,204 
• Modelled Residue Count: 251 
• Deposited Residue Count: 325 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A	325	Homo sapiens	Mutation(s): 0  Gene Names: TYMS, TS, OK/SW-cl.29 EC: 2.1.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for P04818 (Homo sapiens) Explore P04818  Go to UniProtKB:  P04818
PHAROS:  P04818 GTEx:  ENSG00000176890

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9MZ	E [auth A]	2-{(5S)-2-[(2E)-2-(2-hydroxybenzylidene)hydrazinyl]-4-oxo-4,5-dihydro-1,3-thiazol-5-yl}-N-[3-(trifluoromethyl)phenyl]acetamide C19 H15 F3 N4 O3 S OBVIGUGYWMTZGZ-MQEPLNOPSA-N
0MZ	D [auth A]	2-{(2Z,5S)-4-hydroxy-2-[(2E)-(2-hydroxybenzylidene)hydrazinylidene]-2,5-dihydro-1,3-thiazol-5-yl}-N-[3-(trifluoromethyl)phenyl]acetamide C19 H15 F3 N4 O3 S OBVIGUGYWMTZGZ-MQEPLNOPSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.229 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.747	α = 90
b = 95.747	β = 90
c = 82.407	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Tochowicz, A., Finer-Moore, J., Stroud, R.M., Costi, M.P.

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary