4E28 | pdb_00004e28

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.

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1021/jm300850v
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04818
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9MZ Query on 9MZ Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
0MZ Query on 0MZ Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	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		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on 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 (Depositor)
R-Value Work: 0.188 (Depositor)
R-Value Observed: 0.190 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-11-14

Deposition Author(s):

Revision History (Full details and data files)

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