Small Molecule Collections

Bioactive Collections 

YCMD has a number of focused compound collections with known bioactivity.  See below for descriptions.

  • Selleckchem Kinase Inhibitor Library. A unique collection of 418 inhibitors targetting a wide variety of kinases. Contains many kinase drugs and drug-like compounds. 
  • MicroSource Gen-Plus
    960 compounds arrayed in three 384-well plates. Collection includes small molecules with known bioactivity, including medicines currently in use, and is an excellent library for pilot screening because compounds identified in the collection are often known effectors of the assay or operate through intriguing related pathways.
  • MicroSource Pure Natural Products
    800 compounds arrayed in three (one half-filled) 384-well plates. Collection includes characterized alkaloids, flavanoids, sterols, terpenes, stilbenes and more!
  • NIH Clinical Collection
    446 compounds arrayed in two (one half-filled) 384-well plates. Compounds have a history of use in human clinical trials with known safety profiles.
  • NCI Oncology Set 2
    85 compounds at 10 mM concentration arrayed in a single 384-well plate. This collection includes the most current FDA-approved anticancer drugs and enables cancer research and drug discovery.
  • NCI Diversity Set 2
    1356 compounds at 10 mM concentration arrayed in five 384-well plates. This set represents the structural diversity of compounds in the National Cancer Institute’s 140,000 compound collection, available for distribution through the Developmental Therapeutic Program repository.
  • NCI Mechanistic Diversity Set
    774 compounds at 1 mM concentration arrayed in three 384-well plates. This collection was derived from over 37,000 compounds tested in the NCI human tumor 60 cell line screen, and selected to represent a unique profile of growth inhibition relative to other compounds tested (in the 60 cell line screen. )
  • NCI Natural Products Set
    115 compounds at 500 uM arrayed in a single 384-well plate. Natural products were isolated from plants and marine invertebrates from more than 25 tropical and subtropical countries worldwide.
  • Enzo Epigenetics Library
    43 compounds arrayed in one quadrant of a single 384-well plate. Compounds include histone deacetylase and sirtuin inhibitors and are well-characterized and annotated to their corresponding target classes.
  • Enzo Kinase Inhibitor Library
    80 compounds arrayed in one quadrant of a single 384-well plate. Compounds are well-characterized and annotated to their corresponding target kinase.
  • Enzo Phosphatase Inhibitor Set
    33 known phosphatase inhibitors at 10 mM arrayed in a single 384-well plate. The collection includes inhibitors of important phosphatases such as calcineurin (PP2B), JSP-1, PRL-1, CD45, PP1, PRL-3, CDC25, PP2A, PTEN, and more. The set is ideal for assay validation, and as a reference set for secondary screening.
  • MicroSource Pharmakon 1760
    Pharmakon-1760 combines 1360 US and 400 International drugs into one collection on six 384-well plates at 10 mM. The US Drug Collection is comprised of FDA approved drugs as evidenced by their assignment of USP and USAN status and their inclusion in the US Pharmacopeia of Drugs. The International Drug Collection expands the scope of these test constituents by including those drug substances that are used in Europe or Asia but not approved for use in the United States.
  • MicroSource Pharmakon 1600
    1600 compounds arrayed in five 384-well plates at 10 mM concentration. This collection contains 1600 known drugs from US and International Pharmacopeia, where all compounds have reached clinical evaluation and most of the constituent drugs are still in the market. Data provided for each compound define its structure, CAS #, formula, molecular weight, biological profile and generic & market name. For some compounds literature and toxicology information is also available. This set significantly overlaps with the newer MicroSource Pharmakon 1760 collection.
  • Enzo Ion Channel Ligand Library
    The Ion Channel Ligand Library contains 71 ion channel blockers and openers for use in characterizing and identifying ion channels in individual cells or tissue. The compounds arrayed in one quadrant of a single 384-well plate at 10 mM concentration.
  • Enzo Bioactive Lipid Library
    This library contains 197 bioactive lipids arrayed on one 384-well plate format at 1.0 or 0.1mM concentration, depending on compound. The library is good for screening or identifying recombinant orphan G protein-coupled receptors, target validation, secondary screening, validating new assays and for routine pharmacological applications. The library contains some known agonists & antagonists, endocannabinoids, farnesyl/geranylgeranyl derivates, HETEs deHETEs, hepoxilins, polyunsaturated fatty acids, leukotrienes, lipoxins, LPA & phosphatidic acids, octadecanoids, PAFs, prostaglandins & thromboxanes, retinoids, vitamin D metabolites, sphingolipids.
  • Enzo Metabotropic Glutamatergic Ligand Library
    The Metabotropic Glutamatergic Ligands Plate contains 54 ligands including endogenous neurotransmitters, agonists, antagonists, and marketed drugs. The library is good for screening or identifying recombinant orphan G protein coupled receptors, target validation, secondary screening, assay development, and other pharmacological applications. Compounds from this library are provided at 10 mM on a single 384-well plate.
  • Nuclear Receptor Ligand Library
    The Nuclear Receptor Ligand Library contains 76 compounds with defined, putative and potential activity at nuclear receptors, supplied at 10 mM concentration and arrayed into a quadrant on a single 384-well plate. Known receptor agonists and antagonists are included. The library is an ideal tool for chemical genomics, receptor de-orphaning and other routine pharmacological applications.
  • Protease Inhibitor Library
    The Protease Inhibitor Library includes 53 known protease inhibitors arrayed in one quadrant of a 384-well plate at 10 mM concentration. The library includes inhibitors to a broad range of important proteases and is a convenient and cost-effective way to purchase a panel of protease inhibitors for chemical genomics, assay development, and other applications. It includes inhibitors of: Calpains, TPPII, Neutrophil Elastase, Cathepsins, DPPIV, Caspases, Granzyme B, γ-Secretase, Furin, MMPs, ACE, Kallikrein, Proteasome, Aminopeptidase B, and several others.
  • Enzo 640 FDA-approved drugs
    This library consists of two 384-well plates containing 640 compounds total at 10 mM concentration. All compounds have known bioactivity, safety & bioavailability.
  • Tested in Humans Collection

    Our “Tested in Humans” collection currently contains over 90% of medicinally important compounds approved in various regulatory agencies throughout the world (World Appproved Drugs) and which meet certain criteria for screenability. Our “Tested in Humans” collection continues to grow as we add additional compounds with known pharmacology in humans, primarily those compounds with an INN name (International Non-proprietary Name). This collection also includes nutraceuticals such as amino acid supplements. This library consists of eight 384-well plates containing 2,193 compounds at 10 mM concentration.

  • Analyticon

    The Analyticon “Natural Product-like” collection consists of 5000 compounds enriched in sp3 carbon content and inspired by natural products fragments. The Macrocycle collection is 2046 synthetic non-peptide macrocycles comprised of five different chemistries.

  • Boehringer Ingelheim Open Source Thirty-one bioactive compounds.

  • Chemical Degraders (1138 compounds total over four 384-well plates, 10 mM stock concentration) Each molecule has two binding regions- a constant domain for degradation machinery binding and a variable domain to explore small changes in chemical structure that alter substrate specificity. When a new protein substrate binds the variable domain with sufficient affinity, it will be degraded, resulting in a phenotypic change for essential functions. Due to smaller size, this library is recommended for cell-based phenotypic screening to increase the number of potential targets. 

Fragment Collections

  • Enamine Covalent Fragments Library. This collection consists of 799 compounds at 200 mM with a diverse core and attached acrylamide. The acrylamide enables the diverse cores to covalently label biological nucleophiles, predominantly sulfur, via a conjugate addition. The advantage of the acrylamide electrophile over other covalent fragment library chemistries is its stability in aqueous media at wide pH and a high specificity for sulfur nucleophiles. This library would be a choice where a reactive site cysteine or a free cysteine in your biological target is predicted to interfere with function. Calculated properties are MW 147-315, ClogP < 3, TPSA 20-92 sq. Angstroms.

  • Maybridge Ro3 LibraryMaybridge Ro3  library contains 2,500 carefully selected fragments, and provides the optimal balance between broad coverage of lead-like diversity space and the number of fragments required to be screened. Key features and benefits include Rule of Three (Ro3) compliance, increased diversity, experimentally measured solubility (1 mM solubility in PBS guaranteed), exceptional chemical matter quality and purity, and chemical functionality selected to allow rapid chemical evolution and optimization of fragment hits. Collection is eight 384-well plates.

Synthetic Collections 

YCMD has assembled almost 300,000 synthetic small molecules from a variety of different commercial vendors.  Selection of compound collections aimed to optimize diversity and chemical space, and retain drug like characteristics.

  • Life Chemicals Diversity. This unique and highly curated non-proprietary collection consists of 126,320 compounds which should serve as excellent drug leads and molecular probes. The library was selected from approximately 2 million available compounds to meet stringent criteria including ClogP < 5, TPSA 35 - 100 Angstroms and MW 300 - 450. The collection was also filtered to exclude pan assay interference compounds (PAINS) and compounds with reactive, unstable and other undesirable functionalities.  

  • Life Chemicals FSP3. A collection of 25,246 compounds with a high percentage of sp3 (more 3D-like) versus sp2 (more planar) carbons. This collection represents a very high-quality set for lead finding with low aromatic character. The library compounds were selected within a narrow range of lead-like and drug-like properties and meet stringent physico-chemical criteria: MW 250-600, ClogP < 5, TPSA < 140 Angstroms sq., number of hydrogen bond donors <5, sp3/sp2 fraction above 0.45.  The collection was also filtered to exclude pan assay interference compounds (PAINS) and compounds with reactive, unstable and other undesirable functionalities.

  • ChemBridge MicroFormats
    20,000 compounds arrayed in 63, 384-well plates. Collection considers 60 proprietary chemical filters and Daylight Tanimoto similarity measures to assure structural diversity within the set.

  • ChemBridge CNS-Set
    4,960 compounds arrayed in 16, 384-well plates. This collection of small molecules increases the probability of finding hits with oral bio-availability and blood-brain penetration.
  • ChemBridge MW-Set
    10,000 compounds arrayed in 32, 384-well plates. Collection of compounds with small molecular weights (250-450 D) to provide room for further derivatization.
  • ChemBridge DIVERSet
    15,040 compounds arrayed in 48, 384-well plates. Collection is rationally selected to represent the broadest region of biologically relevant pharmacophore diversity space.
  • ChemBridge primary alcohols and aromatic amines
    5,000 compounds arrayed in 16, 384-well plates. Collection of primary alcohols and aromatic amines used in small molecule microarray developmental studies.
  • ChemDiv Library
    64,584 compounds arrayed in 204, 384-well plates. Collection includes 50,000 molecules representing the scaffolds synthesized by ChemDiv, and 15,000 compounds selected to have at least one primary amine, secondary amine, or primary alcohol, which are also used in small molecule microarray developmental studies.
  • Maybridge Diversity
    20,000 compounds arrayed in 63, 384-well plates. Collection is a chemically diverse library that has been filtered for those chemical properties consistent with oral availability (small size, numbers of hydrogen bond donors and acceptors).