Evidence map›Paper›PMID 26327386›Full record

ArticleActa crystallographica. Section D, Biological crystallography2015

Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.

Ivan Shabalin, Zbigniew Dauter, Mariusz Jaskolski, Wladek Minor, Alexander Wlodawer

Open access · bronzeAbstract read
In one paragraph

Article in Acta crystallographica. Section D, Biological crystallography, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.

0numbers the graph read from it
0cells of the map it votes in
36citing papers in PubMed
4.5field-weighted citation impact, top 4% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

36 citing papers in PubMed, 60 citations in OpenAlex.

  1. Duplicate entries in the Protein Data Bank: how to detect and handle them.Acta crystallographica. Section D, Structural biology · 2025
    Article
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  3. Towards a dependable data set of structures for L-asparaginase research.Acta crystallographica. Section D, Structural biology · 2024
    Article
  4. Article
  5. Review
  6. Article
  7. Article
  8. Article
  9. Article
  10. The Affinity of Carboplatin to B-Vitamins and Nucleobases.International journal of molecular sciences · 2021
    Article
  11. Article
  12. Synchrotron Radiation as a Tool for Macromolecular X-Ray Crystallography: a XXI Century Perspective.Nuclear instruments & methods in physics research. Section B, Beam interactions with materials and atoms · 2021
    Article
  13. Article
  14. Article
  15. Article
  16. A close look onto structural models and primary ligands of metallo-β-lactamases.Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy · 2018
    Review
  17. Article
  18. Article
  19. Article
  20. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors at 4 institutions in 2 countries.

Ivan ShabalinDepartment of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA.
Zbigniew DauterSynchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.
Mariusz JaskolskiDepartment of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.
Wladek MinorDepartment of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA.
Alexander WlodawerProtein Structure Section, MCL, National Cancer Institute, Frederick, MD 21702, USA.
University of Virginia · USArgonne National Laboratory · USInstitute of Bioorganic Chemistry, Polish Academy of Sciences · PLNational Cancer Institute · US

Funding

Core H: MicrobiologyU54GM093342 · NIGMS · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI CRONAN, JOHN E. · 2010 to 2015
$34.6M
Midwest Center for Structural GenomicsU54GM094585 · NIGMS · UNIVERSITY OF CHICAGO · PI MINOR, WLADEK · 2010 to 2014
$33.7M
The NYSGRC: A Large Scale Center for PSI:BiologyU54GM094662 · NIGMS · ALBERT EINSTEIN COLLEGE OF MEDICINE, INC · PI FISER, ANDRAS · 2010 to 2014
$32.6M
Macromolecular Crystallography Research with Synchrotron RadiationZIABC010378 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI DAUTER, ZBIGNIEW · 2009 to 2020
$18.8M
Metal binding sites in macromolecular structuresR01GM117325 · NIGMS · UNIVERSITY OF VIRGINIA · PI MINOR, WLADEK · 2016 to 2019
$1.3M
Intramural NIH HHSNIAID NIH HHS HHSN272200700058CNIGMS NIH HHS GM093342NIGMS NIH HHS GM094585NIGMS NIH HHS GM094662NIGMS NIH HHS R01 GM117325NIGMS NIH HHS U54 GM093342NIGMS NIH HHS U54 GM094585NIGMS NIH HHS U54 GM094662
6 · The paper itself

Abstract

The anticancer activity of platinum-containing drugs such as cisplatin and carboplatin is considered to primarily arise from their interactions with nucleic acids; nevertheless, these drugs, or the products of their hydrolysis, also bind to proteins, potentially leading to the known side effects of the treatments. Here, over 40 crystal structures deposited in the Protein Data Bank (PDB) of cisplatin and carboplatin complexes of several proteins were analysed. Significant problems of either a crystallographic or a chemical nature were found in most of the presented atomic models and they could be traced to less or more serious deficiencies in the data-collection and refinement procedures. The re-evaluation of these data and models was possible thanks to their mandatory or voluntary deposition in publicly available databases, emphasizing the point that the availability of such data is critical for making structural science reproducible. Based on this analysis of a selected group of macromolecular structures, the importance of deposition of raw diffraction data is stressed and a procedure for depositing, tracking and using re-refined crystallographic models is suggested.

Indexed as

Antineoplastic AgentsCarboplatinCisplatinCrystallography, X-RayLigandsMolecular StructureProteinsAntineoplastic AgentsCarboplatinCisplatinLigandsProteinscarboplatincisplatincrystal structuredata reprocessingerror correctionsreproducibilitystructural databasesstructure re-refinementvalidation

Identifiers

PMID26327386
PMCPMC4556316
OpenAlexW2170534556

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.