ArticleACS chemical biology2015
The Recognition of Identical Ligands by Unrelated Proteins.
Article in ACS chemical biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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.
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.
Who cites it
30 citing papers in PubMed.
- Comprehensive detection and characterization of human druggable pockets through binding site descriptors.Nature communications · 2024Article
- Pan-HSP90 ligand binding reveals isoform-specific differences in plasticity and water networks.Protein science : a publication of the Protein Society · 2023Article
- Mining the Protein Data Bank to inspire fragment library design.Frontiers in chemistry · 2023Article
- Classification of Protein-Binding Sites Using a Spherical Convolutional Neural Network.Journal of chemical information and modeling · 2022Article
- Estimating the Similarity between Protein Pockets.International journal of molecular sciences · 2022Review
- Discovery of Kinase and Carbonic Anhydrase Dual Inhibitors by Machine Learning Classification and Experiments.Pharmaceuticals (Basel, Switzerland) · 2022Article
- Set-Theoretic Formalism for Treating Ligand-Target Datasets.Molecules (Basel, Switzerland) · 2021Article
- Repurposing approved drugs on the pathway to novel therapies.Medicinal research reviews · 2020Review
- Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies.Journal of computer-aided molecular design · 2019Article
- High Impact: The Role of Promiscuous Binding Sites in Polypharmacology.Molecules (Basel, Switzerland) · 2019Article
- Article
- DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network.PLoS computational biology · 2019Article
- Privileged Structures and Polypharmacology within and between Protein Families.ACS medicinal chemistry letters · 2018Article
- A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs).PLoS computational biology · 2018Article
- The Recognition of Unrelated Ligands by Identical Proteins.ACS chemical biology · 2018Article
- Docking Screens for Dual Inhibitors of Disparate Drug Targets for Parkinson's Disease.Journal of medicinal chemistry · 2018Article
- Redesign of LAOBP to bind novel l-amino acid ligands.Protein science : a publication of the Protein Society · 2018Article
- Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases.PLoS computational biology · 2018Article
- Comparative assessment of strategies to identify similar ligand-binding pockets in proteins.BMC bioinformatics · 2018Article
- How to Achieve Better Results Using PASS-Based Virtual Screening: Case Study for Kinase Inhibitors.Frontiers in chemistry · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
The binding of drugs and reagents to off-targets is well-known. Whereas many off-targets are related to the primary target by sequence and fold, many ligands bind to unrelated pairs of proteins, and these are harder to anticipate. If the binding site in the off-target can be related to that of the primary target, this challenge resolves into aligning the two pockets. However, other cases are possible: the ligand might interact with entirely different residues and environments in the off-target, or wholly different ligand atoms may be implicated in the two complexes. To investigate these scenarios at atomic resolution, the structures of 59 ligands in 116 complexes (62 pairs in total), where the protein pairs were unrelated by fold but bound an identical ligand, were examined. In almost half of the pairs, the ligand interacted with unrelated residues in the two proteins (29 pairs), and in 14 of the pairs wholly different ligand moieties were implicated in each complex. Even in those 19 pairs of complexes that presented similar environments to the ligand, ligand superposition rarely resulted in the overlap of related residues. There appears to be no single pattern-matching "code" for identifying binding sites in unrelated proteins that bind identical ligands, though modeling suggests that there might be a limited number of different patterns that suffice to recognize different ligand functional groups.
Indexed as
Identifiers
What OpenQuestion holds
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.