Evidence map›Paper›PMID 40856436›Full record

ArticleActa crystallographica. Section F, Structural biology communications2025

Off-target binding of the histone deacetylase inhibitor vorinostat to carbonic anhydrase II and IX.

Mitchell C Gulkis, James T Hodgkinson, Céleste P Sele, Wolfgang Knecht, Robert McKenna, S Zoë Fisher

Abstract read
In one paragraph

Article in Acta crystallographica. Section F, Structural biology communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
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

2 citing papers in PubMed.

  1. Review
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Mitchell C GulkisDepartment of Biochemistry and Molecular Biology, University of Florida, 1149 Newell Drive, Gainesville, FL 32610, USA.ORCID 0000-0001-5831-8802
James T HodgkinsonLeicester Institute of Structural and Chemical Biology and School of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom.ORCID 0000-0001-9978-7322
Céleste P SeleLund Protein Production Platform and Protein Production Sweden, Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.ORCID 0000-0003-4916-3065
Wolfgang KnechtLund Protein Production Platform and Protein Production Sweden, Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.ORCID 0000-0001-9530-7598
Robert McKennaDepartment of Biochemistry and Molecular Biology, University of Florida, 1149 Newell Drive, Gainesville, FL 32610, USA.ORCID 0000-0002-2792-935X
S Zoë FisherLund Protein Production Platform and Protein Production Sweden, Department of Biology, Lund University, Sölvegatan 35, 22362 Lund, Sweden.ORCID 0000-0001-8287-0269

Funding

ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale ModelingR01GM129325 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FERRIN, THOMAS E · 2018 to 2025
$5.2M
NIGMS NIH HHS R01 GM129325
6 · The paper itself

Abstract

Histone deacetylase inhibitors (HDACi) are widely used in cancer therapy but often suffer from off-target effects due to their pan-inhibitory activity towards zinc-dependent enzymes. Vorinostat (SAHA), a hydroxamate-based HDACi, has been shown to lack isoform selectivity, potentially leading to unintended interactions with other metalloenzymes. Here, we report high-resolution crystal structures of SAHA bound to human carbonic anhydrase II (CA II) and a carbonic anhydrase IX (CA IX) active-site mimic. Structures determined at room temperature and 100 K revealed two distinct SAHA conformers in both CA II and the CA IX mimic, with the hydroxamate moiety displacing the zinc-bound water and adopting either a tetrahedral or pentahedral coordination to Zn

Indexed as

Antigens, NeoplasmCarbonic Anhydrase IICarbonic Anhydrase IXHistone Deacetylase InhibitorsVorinostatBinding SitesCatalytic DomainCrystallography, X-RayHumansHydroxamic AcidsModels, MolecularMolecular Docking SimulationProtein BindingZincAntigens, NeoplasmCA9 protein, humanCarbonic Anhydrase IICarbonic Anhydrase IXHistone Deacetylase InhibitorsHydroxamic AcidsVorinostatZincHDAC inhibitorshuman carbonic anhydrasesoff-target bindingSAHAvorinostat

Identifiers

PMID40856436
PMCPMC12400194

What Socratic holds

Textmetadata
LicenceCC BY
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 Socratic graph.