ArticleNucleic acids research2010
Structural signatures of antibiotic binding sites on the ribosome.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 34 citations in OpenAlex.
- Quantum Chemical Insights into Antibiotic Structure-Activity Relationships and Mechanisms of Action: A Review.Molecules (Basel, Switzerland) · 2026Review
- Exploring Secondary Structure Predictions for RNA-Targeted Drug Discovery: Power and Challenges.Journal of chemical information and modeling · 2026Article
- DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning.Nucleic acids research · 2025Article
- Pyrosequencing analysis for rapid and accurate detection of clarithromycin resistance-associated mutations in Iranian Helicobacter pylori isolates.BMC research notes · 2023Article
- An Evolutionary Conservation and Druggability Analysis of Enzymes Belonging to the Bacterial Shikimate Pathway.Antibiotics (Basel, Switzerland) · 2022Article
- Augmented base pairing networks encode RNA-small molecule binding preferences.Nucleic acids research · 2020Article
- Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit.Nucleic acids research · 2020Article
- Translation: The Universal Structural Core of Life.Molecular biology and evolution · 2018Article
- Exploring allosteric communication in multiple states of the bacterial ribosome using residue network analysis.Turkish journal of biology = Turk biyoloji dergisi · 2018Article
- Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM.Nature · 2015Article
- The role of RNA conformation in RNA-protein recognition.RNA biology · 2015Article
- Regulation of gene expression by macrolide-induced ribosomal frameshifting.Molecular cell · 2013Article
- Conformational readout of RNA by small ligands.RNA biology · 2013Article
- Allosteric control of the ribosome by small-molecule antibiotics.Nature structural & molecular biology · 2012Article
- Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ribosome represents a major target for antibacterial drugs. Being a complex molecular machine, it offers many potential sites for functional interference. The high-resolution structures of ribosome in complex with various antibiotics provide a unique data set for understanding the universal features of drug-binding pockets on the ribosome. In this work, we have analyzed the structural and evolutionary properties of 65 antibiotic binding sites (ABSs) in the ribosome. We compared these sites to similar-size computed pockets extracted from the small and large ribosomal subunits. Based on this analysis, we defined properties of the known drug-binding sites, which constitute the signature of a 'druggable' site. The most noticeable properties of the ABSs are prevalence of non-paired bases, a strong bias in favor of unusual syn conformation of the RNA bases and an unusual sugar pucker. We propose that despite the different geometric and chemical properties of diverse antibiotics, their binding sites tend to have common attributes that possibly reflect the potency of the pocket for binding small molecules. Finally, we utilized the ensemble of properties to derive a druggability index, which can be used in conjunction with site functionality information to identify new drug-binding sites on the ribosome.
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Registered trials
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.