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Compound collections and or compound macromolecule data or annotated cmpds

some key websites to find chemical vendors...




NALDB Nucleic acid ligand database for small molecules targeting nucleic acid (2016)


DrugCentral Online drug compendium (2016)


KLIFS A structural kinase-ligand interaction database


PDEStrIAn A Phosphodiesterase Structure and Ligand Interaction Annotated Database


FooDB FooDB is the world’s largest and most comprehensive resource on food constituents, chemistry and biology. It provides information on both macronutrients and micronutrients, including many of the constituents that give foods their flavor, color, taste, texture and aroma


GLASS GPCR-Ligand Association database


CancerResource CancerResource-updated database of cancer-relevant proteins, mutations and interacting drugs database
Metabolomics Workbench An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools


CancerHSP Anticancer herbs database of systems pharmacology (natural products)


SCUBIDOO Screenable Chemical Universe Based on Intuitive Data OrganizatiOn (SCUBIDOO). 21 million virtual products originating from a small library of building blocks and a collection of robust organic reactions

database for in silico screening

Chemical probes Molecular Libraries Probes (NIH probes dataset on Molsync) MLP Probes chemical probes database
DrugBank DrugBank, list of drugs, experimental structures...In 2014, many novel information about drug metabolism database
EpiDBase A manually curated database for small molecule modulators of epigenetic landscape (about 5000 cmpds in 2015) database
CFam A chemical families database based on iterative selection of functional seeds and seed-directed compound clustering (2015) database
CoCoCo It is a suite of molecular databases for high throughput virtual screening purposes database
DTP Anti-cancer Agent Mechanism Database (122 molecules) with reasonably well known mechanism of action (NCI-NIH). Development therapeutic program database
EDULISS A small-molecule database with data-mining and pharmacophore searching capabilities database
HIT Linking herbal active ingredients to targets, natural products.Derived from more than 3250 literatures, it currently contains 5208 entries about 1301 known protein targets (221 of them are described as direct targets) affected by 586 herbal compounds from more than 1300 reputable Chinese herbs, overlapping with 280 therapeutic targets from Therapeutic Targets Database (TTD), and 445 protein targets from DrugBank corresponding to 1488 drug agents. The database can be queried via keyword search or similarity search database
NutriChem NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods database
Chemical probes Molecular Libraries Probes MLP Probes database 
ZENODO The ZENODO platform contains annoted compounds for several targets (Bajorath group 2014) database
iSMART It is a multi-functional cloud-computing web system that comprised with three components: (1) TCM Database@Taiwan, (2) iScreen, for virtual screening, and (3) iSplice. Natural products based on components from traditional Chinese medicines

database online


Pediatrics Expanding the scope of drug repurposing in pediatrics: The Children s Pharmacy Collaborative. A database of small molecules for children in a SDF file in the supplement data dataset to download
Allostery Allosteric molecules at Chembl dataset to download
Find Compounds iScienceSearch most typical applications: For what is my compound useful? Find suppliers for lab and research chemicals. Search the AKosSamples database by substructure. Search the Internet by drawing a structure. Type a name and you get the structure. Search patents. A kind of Google for chemistry. Also ADMET information online
Drug Databases Medi-Span provides a number of clinical files or modules intended to support safety screening, clinical decision support, and other functions across healthcare applications (commercial) database
NAPRALERT A relational database of all natural products including molecules used in Ayurvedic medicine (traditional medicine, Ayurveda) database
FRLHT Foundation for Revitalisation of Local Health Traditions. Natural products including molecules used in Ayurvedic medicine (traditional medicine, Ayurveda) database
Selleckchem Chemical compounds some with numerous annotations (including preclinical data), some dedicated to targets...(Selleck Chemicals)

database online

TCMSP A database of systems pharmacology for drug discovery from herbal medicines database
ODORactor An open access web server aimed at providing a platform for identifying odorant receptors (ORs) for small molecules and for browsing existing OR-ligand pairs database - online tool
UniChem Chemical structure integration across a large number of public resources database - online
BARD The powerful new bioassay database from the NIH Molecular Libraries Program database
Surechem SureChEmbl: Chemical structures from patents

database - online

ZINClick A Database of 16 Million Novel, Patentable, and Readily Synthesizable 1,4-Disubstituted Triazol database
SM2miR A database of experimentally validated small molecules effects on microRNA expression database
SuperScent A database of flavors and scents database
MCSS A multi-fingerprint browser for the ZINC database. To confirm the activity of an initial small molecule hit compound from an activity screening, one needs to probe the structure–activity relationships by testing close analogs. The multi-fingerprint browser assists this process

database and search tool

Flavornet Flavornet and human odor space database
fragrance Expanding the fragrance chemical space for virtual screening, SuperScent and Flavornet were analyzed to define a fragrance-like (FL) property range. Diverse collections were analyzed with this FL filter and the FL-mapplet and FL-browser were created database
Orange Book Approved Drug Products with Therapeutic Equivalence Evaluations database
Drug2Gene A knowledge base (reported 2014), which combines the compound drug-gene protein information from 19 publicly available databases database
Database PROCOGNATE is a database of protein cognate ligands for the domains in enzyme structures as described by CATH, SCOP and Pfam, and is available as an interactive website or a flat file database
AnalytiCon Analyticon Discovery GmbH: Natural product company database online
EGFRIndb Epidermal Growth Factor Receptor Inhibitor Database database
SMMRNA An interactive database with special focus on small molecule ligands targeting RNA. Currently, SMMRNA consists of 770 unique ligands along with structural images of RNA molecules database
e-LEA3D e-Drug3D: Chemical content of the collection of commercial fragments (privileged structures) extracted from the FDA approved drugs online
AfroDb A Select Highly Potent and Diverse Natural Product Library from African Medicinal Plants (about 1000 molecules) database
pan-ANAPL pan-African Natural Products Library ask the authors, the link does not seem to work
QCL Nature Bank and the Queensland Compound Library: Unique International Resources at the Eskitis Institute for Drug Discovery database
MAPS Medicinal plant Activities, Phytochemical and Structural Database database
CVDHD A cardiovascular disease herbal database for drug discovery and network pharmacology database
DNP Dictionary of Natural Products database
HEMD An integrated tool of human epigenetic enzymes and chemical modulators for therapeutics database
WebCSD The world's online portal to the Cambridge Structural Database database
LINK Collection for FBDD/FBLD : commercial fragments (privileged strutures) extracted from FDA approved drugs database
HEI A database of high energy intermediates for docking datasets
BIAdb A Database for Benzylisoquinoline Alkaloids database
BitterDB  A database of about 570 bitter compounds database
StreptomeDB A resource for natural compounds isolated from Streptomyces species       database
NPACT Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database       database
SuperNatural A searchable database of available natural compounds (around 2015, Super Natural II, over 325500 natural compounds)    

database - online

UNPD  Universal natural products database in May 2013, about 197201 natural products from plants, animals and microorganisms       database
KIDFamMap A database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms        database
CBID or CBID is a Web-interfaced cannabinoid molecular information database repository that are designed and constructed to facility data-sharing and information exchange among scientific research communities with online structure search functions and data analysis tools implemented database
CamMedNP  Building the Cameroonian 3D structural natural products database for virtual screening, Fidele Ntie-Kang et al., BMC Complementary and Alternative Medicine 2013, contact the authors and check the supplement file. Over 2500 molecules database
Xemistry Interactive Quantitative Structure Fragmentation


Xemistry Chemical Structure Algorithm consistency verification service online
SciFinder  Provides researchers with unlimited access to the world s largest and most reliable collection of chemistry and related science information commercial
Reaxys  A web-based search and retrieval system for available chemical compounds. Reaxys gathers three separate databases spanning organic chemistry, organometallic and inorganic chemistry of chemical patents, and contains reaction and substance data, as well as experimentally measured properties commercial
Assistant ScreeningAssistant 2 is a free and open-source desktop software dedicated to store and manage chemical libraries in a local or network-accessible MySQL database, and perform various analysis using simple and advanced chemoinformatics methods. Linux and Windows Tool to prepare collection, standalone
SPORES Structure PrOtonation and REcognition System standalone
LINK KODE solutions istMolBase: dataset management (reading of SMILES and SDF files, depiction, molecule normalization, SMARTS matching), istChemFeat: dataset analysis by means of relevant chemical features research standalone
CLEVER  Chemical library editing, visualizing and enumerating resource: tool to manage collection standalone
LINK looking at SMARTS

SMARTS chemoinfo


OlfactionDB Odorants are molecules that efficiently carry chemical information, providing one of the main ways for communicating with the environment in all kingdoms of life. In the other hand, mammalian genomes codify for hundreds of olfactory receptors (OR), underlying the crucial role of the sense of smell during evolution, being able to discriminate about 10000 different odors database
LIPIDMAPS  Provides a range of tools and resources to facilitate lipid research database
LINK French compound collection - CNRS database, need to register
AutoClick Chem Performs many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization standalone
Chemical space ScaffoldTreeGenerator Chemoinformatics - navigation in chemical space  standalone
SeRAPhiC Data set of 53 high-quality protein-fragment complexes  dataset
BAPPL 161 protein-ligand complexes with experimental and estimated binding free energies dataset
SMPDB Small Molecule Pathway Database is an interactive, visual database containing more than 350 small molecule pathways found in humans database
GDB-11  Enumerates small organic molecules up to 11 atoms of C, N, O and F following simple chemical stability and synthetic feasibility rules, other related databases, peptides

virtual database online & other related tools

LINK Chemical structure lookup search in search in 74 million indexed structures from over 100 databases (46 million unique structures) database
ClinicalTrials  A registry of federally and privately supported clinical trials conducted in the United States and around the world. gives you information about a trial's purpose, who may participate, locations, and phone numbers for more details. This information should be used in conjunction with advice from health care professionals


LINK Animal drugs database
LINK FDA Animal drugs: Electronic Animal Drug Product Listing Directory database
AMDD  Antimicrobial Drug Database: 2900 antibacterial and 1200 antifungal database
LINK open drug database database
ChemBank Free collections and utilities, known drugs, many annotated molecules, molecules with druglike and non-druglike properties

Compound Database, Compound searching, prescription drugs online

PubChemDB PubChemDB is a Java API for working with PubChem data-sets Database online
PubChem An information resource linking chemistry and biology

Database online

LINK  Chemical thesaurus : database including chemical entities, interactions, reactions, processes Compound Database online
LINK Chemical suppliers and collections Compound Database online
LINK Web directory about compound collections and many related links, database search (bioscreening)

Compound Database, Compound searching online

LINK Free collections if you collaborate with the group Compound Database, part of the French National Compound collection
LINK Free collections KEGG ligand database

Compound Database, online

LINK Crystallography Open Database

compounds in 3D, database

NMRShiftDB  Free collection, some molecules are in 3D Compound Database
NMRShiftDB NMRShiftDB Compound Database
ZINC Free collections (and links to many commercial vendors), also natural products

Compound Database, ADME/Tox, Compound searching

DUD-E The complete DUD-E benchmarking set, the more recent DUD, 2012 datasets
DUD DUD is designed to help test docking algorithms by providing challenging decoys Compounds for different targets, thrombin, FXa...and decoys, datasets
ChemMine  Free collections and similarity search utilities, clustering

Compound Database, Compound searching, online

navigator Chemnavigator: Commercial collection

Compound Database, Compound searching, online

ChEBI Dictionary of small molecules. ChEBI: a database and ontology for chemical entities of biological interest

Compound Database, online

LINK DNA-DRUG complex dataset Compound Database and Macromolecules
NuBBEDB NuBBE database is a virtual database of natural products and derivatives from Brazilian biodiversity Compound Database
BindingDB Measured binding affinities, macromolecule-ligand complexes

Compound Database, Macromolecules, online

MOAD Binding MOAD (Mother of All Databases)

Compound Database, Macromolecules, online


SIDER  Contains information on marketed medicines and their recorded adverse drug reactions. Profiling

profiling, ADMETox, database, online

STITCH     Interaction networks of chemicals and proteins. Profiling. Genomes, about 2200 drugs, 68000 chemicals Compound Database, Macromolecules, online
LPDB LPDB database: ligand-protein Drug-Ligand Database
MMsINC  A database of non-redundant, richly annotated, and biomedically relevant chemical structures             Drug Database, online
SMILIB  Tool to create virtual libraries Virtual Database generator in smiles, standalone
GLARE  Generate combinatorial library standalone
Newlead Generate of combinatorial library from bioactive conformations standalone
sMOL Explorer A 2D ligand-based computational tool that provides three major functionalities: data management, information retrieval and extraction, and statistical analysis and data mining through Web interface. It is an open source, web-enabled database and exploration tool for Small MOLecules datasets, Bioinformatics Data managment - Web interface small molecules
e-LEA3D            De novo drug design tool, drugs approved on the market           

de novo screening scaffold-hopping combinatiorial library design, online

Ilib Diverse Tool to create virtual drug-like libraries Virtual Database generator, standalone
LINK The US National Cancer Institute collections including natural products Compound Database
LINK Main chemical-structures Compound Database, standalone
LINK  View properties, purchase compounds Compound Database
LINK View structures and data of Open NCI DB compounds Compound Database
LINK Find compound properties Compound searching
LINK Similarity search and other tools Compound searching
ChemSpider Compound search, find chemical vendors Compound searching and utilities online
Chembl Database of bioactive molecules

 Annotated database online

LINK The web of chemical informatics Chemistry blog
ChemExper Find chemicals in the ChemExper Chemical Directory

online database

eMolecules With eMolecules you can draw your chemical structure and instantly search millions of molecules from across the Web and from chemical suppliers worldwide. Find chemical vendors

Compound searching online

PDBeChem  Consistent and enriched library of ligands, small molecules and monomers that are referred as residues and hetgroups in any PDB entry

Compound Database from the PDB, Compound searching, X-ray, online

Ligand-Expo Ligand-Expo (formerly Ligand Depot) provides chemical and structural information about small molecules within the structure entries of the Protein Data Bank database
SuperLigands  A database of ligand structures derived from the Protein Data Bank with similarity searches and other tools online
LINK Chemistry and biology database: numerous links (databases, tools) valuable for drug design projects Compound Database, macromolecules links to programs
HIC-Up HIC-Up Hetero-compound Information: Small molecules from the PDB Compound Database from the PDB, online
LINK The directory of chemistry on the WWW since 1993 Numerous chemistry links
LINK Compound collection and building blocks Compound Database online
Prestwick The Prestwick Chemical Library  is a unique collection of about  1120 high-purity chemical compounds (all off patent)  carefully selected Off patent compound collections for experimental testing, online
Spectrum The Spectrum Collection  2000 biologically active and structurally diverse compounds from our libraries of known drugs, experimental bioactives, and pure natural products.  SDF file available Structurally diverse compounds for experimental screening and in silico work, online
SeqChem  Biochemicals and other natural products Compounds for experimental screening
DTP DTP maintains a repository of synthetic and natural products that have been evaluated as potential  anticancer and anti-HIV agents. This repository has an historic inventory of more than 140,000  non-discreet compounds that have been submitted to DTP from a variety of sources worldwide.  Compound collections for experimental or in silico screening
Marvel Marvel Library - A Collection of Over 9000 Unique Compounds database
TCMGeneDIT  Database system providing association information about traditional Chinese medicines (TCMs), genes, diseases, TCM effects and TCM ingredients automatically mined from vast amount of biomedical literature Database online, natural products
TCM TCM Database Taiwan: Largest Traditional Chinese Medicine Database for Drug Screening In Silico Ligand Database online
TCMID  Traditional Chinese Medicine integrative database for herb molecular mechanism analysis Ligand Database online
Indian Plant Indian Plant Anticancer Compounds Database (Ayurvedic medicine, Ayurveda). Does not seem to work Database online (the site is moving and may not work from time to time)
LINK Database on pharmacophore analysis of active principles, from medicinal plants database, server not found, thus link to PUBMED