The NCGC Pharmaceutical Collection (NPC) is a comprehensive, publically-accessible collection of approved and investigational drugs for high-throughput screening that provides a valuable resource for both validating new models of disease and better understanding the molecular basis of disease pathology and intervention. The paper is: R. Huang, N. Southall, Y. Wang, A. Yasgar, P. Shinn, A. Jadhav, D.-T. Nguyen, C. P. Austin, The NCGC Pharmaceutical Collection: A Comprehensive Resource of Clinically Approved Drugs Enabling Repurposing and Chemical Genomics. Sci. Transl. Med. 3, 80ps16 (2011). We are grateful to the authors for creating and curating this database and thank them for allowing us to incorporate its structures in ZINC.
We assess the chemical diversity of a subset by clustering the molecules. First, we sort ligands by increasing molecular weight. Then, we use the SUBSET 1.0 algorithm ( Voigt JH, Bienfait B, Wang S, Nicklaus MC. JCICS, 2001, 41, 702-12) to progressively select compounds that differ from those previously selected by at least the Tanimoto cutoff, using ChemAxon default fingerprints. The resulting representatives have two interesting properties:
|Tanimoto Cutoff Level||60%||70%||80%||90%||100%|
|Number of Representatives||929||1,431||1,868||2,349||3,784|
We compute the physical properties of each molecule in the subset, and graph them below.
Download Calculated Physical Properties
|Format||Reference(pH 7)||Mid(pH 6-8)||High(pH 8-9.5)||Low(pH 4.5-6)||Download
|MOL2||All||All||All||All||Single Usual Metals All||Single Usual Metals All|
|SDF||All||All||All||All||Single Usual Metals All||Single Usual Metals All|
|Flexibase||0 1 2||All||All||All||Single Usual Metals All||Single Usual Metals All|