ArticleMedChemComm2017
A systematic analysis of atomic protein-ligand interactions in the PDB.
Article in MedChemComm, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 192 papers.
What it found
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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.
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Who cites it
192 citing papers in PubMed.
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- Discussions on the generalization of HybridSP on more equivalent benchmarks.Briefings in bioinformatics · 2026Article
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- Uncovering the bactericidal potential of extract and multi-targeting phytochemicals from Mirabilis longiflora L. leaves against multidrug-resistant Pseudomonas aeruginosa and Bacillus cereus.Scientific reports · 2026Article
- Oblique-incidence reflectivity difference technology identifies the antiviral drug Ribavirin as an inhibitor of lung tumor progression by targeting AMPK signaling.Journal of pharmaceutical analysis · 2026Article
- Polynuclear Silver(I)-Quinoxaline Complex: Comprehensive Structural Characterization, Antimycobacterial Properties and DNA/BSA Binding Study.Pharmaceutics · 2026Article
- Parallels between the chloro and methoxy groups for potency optimization.RSC medicinal chemistry · 2026Article
132 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
As the protein databank (PDB) recently passed the cap of 123 456 structures, it stands more than ever as an important resource not only to analyze structural features of specific biological systems, but also to study the prevalence of structural patterns observed in a large body of unrelated structures, that may reflect rules governing protein folding or molecular recognition. Here, we compiled a list of 11 016 unique structures of small-molecule ligands bound to proteins - 6444 of which have experimental binding affinity - representing 750 873 protein-ligand atomic interactions, and analyzed the frequency, geometry and impact of each interaction type. We find that hydrophobic interactions are generally enriched in high-efficiency ligands, but polar interactions are over-represented in fragment inhibitors. While most observations extracted from the PDB will be familiar to seasoned medicinal chemists, less expected findings, such as the high number of C-H···O hydrogen bonds or the relatively frequent amide-π stacking between the backbone amide of proteins and aromatic rings of ligands, uncover underused ligand design strategies.
Identifiers
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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.