6ZXO | pdb_00006zxo

Crystal structure of His-tagged human thymidylate synthase (HT-hTS) in complex with FdUMP and Raltitrexed (Tomudex)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.232 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6ZXO

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural Bases for the Synergistic Inhibition of Human Thymidylate Synthase and Ovarian Cancer Cell Growth by Drug Combinations.

Pozzi, C.Santucci, M.Marverti, G.D'Arca, D.Tagliazucchi, L.Ferrari, S.Gozzi, G.Losi, L.Tassone, G.Mangani, S.Ponterini, G.Costi, M.P.

(2021) Cancers (Basel) 13

  • DOI: https://doi.org/10.3390/cancers13092061
  • Primary Citation Related Structures: 
    6ZXO

  • PubMed Abstract: 

    Combining drugs represent an approach to efficiently prevent and overcome drug resistance and to reduce toxicity; yet it is a highly challenging task, particularly if combinations of inhibitors of the same enzyme target are considered. To show that crystallographic and inhibition kinetic information can provide indicators of cancer cell growth inhibition by combinations of two anti-human thymidylate synthase (hTS) drugs, we obtained the X-ray crystal structure of the hTS:raltitrexed:5-fluorodeoxyuridine monophosphate (FdUMP) complex. Its analysis showed a ternary complex with both molecules strongly bound inside the enzyme catalytic cavity. The synergistic inhibition of hTS and its mechanistic rationale were consistent with the structural analysis. When administered in combination to A2780 and A2780/CP ovarian cancer cells, the two drugs inhibited ovarian cancer cell growth additively/synergistically. Together, these results support the idea that X-ray crystallography can provide structural indicators for designing combinations of hTS (or any other target)-directed drugs to accelerate preclinical research for therapeutic application.


  • Organizational Affiliation
    • Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, Via A. Moro 2, 53100 Siena, Italy.

Macromolecule Content 

  • Total Structure Weight: 227.98 kDa 
  • Atom Count: 14,315 
  • Modeled Residue Count: 1,727 
  • Deposited Residue Count: 1,950 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thymidylate synthase
A, B, C, D, E
325Homo sapiensMutation(s): 0 
Gene Names: TYMSTSOK/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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04818
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Thymidylate synthase325Homo sapiensMutation(s): 0 
Gene Names: TYMSTSOK/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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04818
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D16
(Subject of Investigation/LOI)

Query on D16



Download:Ideal Coordinates CCD File
G [auth A]
J [auth B]
M [auth C]
P [auth D]
R [auth E]
G [auth A],
J [auth B],
M [auth C],
P [auth D],
R [auth E],
T [auth F]
TOMUDEX
C21 H22 N4 O6 S
IVTVGDXNLFLDRM-HNNXBMFYSA-N
UFP
(Subject of Investigation/LOI)

Query on UFP



Download:Ideal Coordinates CCD File
H [auth A]
K [auth B]
N [auth C]
Q [auth D]
S [auth E]
H [auth A],
K [auth B],
N [auth C],
Q [auth D],
S [auth E],
U [auth F]
5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
C9 H12 F N2 O8 P
HFEKDTCAMMOLQP-RRKCRQDMSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
I [auth A],
L [auth B],
O [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
F
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Binding Affinity Annotations 
IDSourceBinding Affinity
D16 BindingDB:  6ZXO IC50: min: 9, max: 2.90e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.232 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.72α = 112.39
b = 95.87β = 91.47
c = 103.84γ = 109.17
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItalyIG10474

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary