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Mcule database

  • Screen in-house and purchase the best virtual hits by just a few clicks
  • Expand your in-house library with unique and diverse compounds
  • High quality database and professional procurement service

You can freely download the following collections of the high quality Mcule database including 2D structures and Mcule IDs:

Subset name Description Last updated Nb. of compounds Filetype Filesize Download
Mcule Full Purchasable Mcule supplier & ULTIMATE catalogs Feb. 17, 2024 41,766,991
2D SDF (sdf.gz)
SMILES (smi.gz)
9.4 GB
531.0 MB
Mcule In Stock Purchasable Mcule supplier in stock catalogs Feb. 18, 2024 5,847,191
2D SDF (sdf.gz)
SMILES (smi.gz)
1.3 GB
86.0 MB
Mcule Full Building Blocks Purchasable Mcule supplier building block catalogs Feb. 18, 2024 4,446,478
2D SDF (sdf.gz)
SMILES (smi.gz)
614.0 MB
55.0 MB
Mcule Known Stock Amounts Purchasable Mcule supplier in stock catalogs with known stock amount Feb. 18, 2024 5,046,534
2D SDF (sdf.gz)
SMILES (smi.gz)
1.2 GB
75.0 MB
Mcule Virtual Purchasable Mcule supplier virtual catalogs & ULTIMATE catalogs Feb. 18, 2024 35,700,485
2D SDF (sdf.gz)
SMILES (smi.gz)
8.1 GB
442.0 MB
Mcule ULTIMATE Express Purchasable Mcule ULTIMATE Express catalogs with fast delivery Aug. 28, 2022 15,618,017
2D SDF (sdf.gz)
SMILES (smi.gz)
3.0 GB
186.0 MB
Mcule ULTIMATE Express 1 Purchasable Mcule ULTIMATE Express 1 catalog with fast delivery Aug. 28, 2022 486,387
2D SDF (sdf.gz)
SMILES (smi.gz)
65.0 MB
6.0 MB

If you need the database in smaller chunks, please visit the documentation site where you can find detailed instructions on how to create smaller files.

Mcule libraries

  • Filtered from catalogs of more than 100 suppliers.
  • Advanced property and substructure filters.
  • Regularly updated.

You can freely download the following libraries filtered from the high quality Mcule database:

Subset name Description Last updated Nb. of compounds Filetype Filesize Download
Mcule RNA-Binding Library Includes compounds that are approved as RNA binders (Layer 1) and those showing high molecular similarity to known RNA binders (Layer 2) Feb. 17, 2024 681,828
PDF flyer
zip
1.0 MB
64.0 MB
Mcule RNA-Binding In Stock Library Includes in stock compounds that are approved as RNA binders (Layer 1) and those showing high molecular similarity to known RNA binders (Layer 2) Feb. 17, 2024 357,861
PDF flyer
zip
1.0 MB
38.0 MB
Mcule Kinase Targeting Library Compounds showing high molecular similarity to known orthosteric protein kinase binders and their regulatory subunits. Feb. 17, 2024 30,484
csv.gz
PDF
PDF flyer
3.0 MB
1.0 MB
1.0 MB
Mcule Kinase Targeting In stock Library In stock compounds showing high molecular similarity to known orthosteric protein kinase binders and their regulatory subunits. Feb. 17, 2024 4,348
csv.gz
PDF
PDF flyer
1.0 MB
1.0 MB
1.0 MB
Mcule Bioactivity Library Phenotypic/Epigenetic/Chemogenomic screening of bioactive compounds with ChEMBL annotations Feb. 17, 2024 20,337
PDF flyer
zip
1.0 MB
2.0 MB
Mcule Bioactivity In stock Library Phenotypic/Epigenetic/Chemogenomic screening of bioactive in stock compounds with ChEMBL annotations Feb. 17, 2024 17,058
PDF flyer
zip
1.0 MB
1.0 MB
Mcule Fragment Library Fragments Feb. 17, 2024 295,115
PDF flyer
zip
1.0 MB
4.0 MB
Mcule In stock Fragment Library In stock fragments Feb. 17, 2024 144,273
PDF flyer
zip
1.0 MB
2.0 MB
Mcule HTS Library ‘True Positive’ High Throughput Screening hits Feb. 17, 2024 1,623,641
PDF flyer
SMILES (smi.gz)
1.0 MB
20.0 MB
Mcule In stock HTS Library ‘In stock True Positive’ High Throughput Screening hits Feb. 17, 2024 515,237
PDF flyer
SMILES (smi.gz)
1.0 MB
7.0 MB
Mcule Molecular Glue Library Small molecules with mostly two binding sites, of which one is the E3 binding substructure. Feb. 17, 2024 25,678
PDF flyer
SMILES (smi.gz)
1.0 MB
1.0 MB
Mcule Molecular Glue In stock Library In stock small molecules with mostly two binding sites, of which one is the E3 binding substructure. Feb. 17, 2024 8,224
PDF flyer
SMILES (smi.gz)
1.0 MB
1.0 MB
Mcule GPCR Targeting Library Compounds that are annotated with the GPCR receptor subfamilies they potentially target Feb. 17, 2024 3,862,576
csv.gz
PDF
PDF flyer
257.0 MB
1.0 MB
1.0 MB
Mcule GPCR Targeting In stock Library In stock compounds that are annotated with the GPCR receptor subfamilies they potentially target Feb. 17, 2024 587,845
csv.gz
PDF
PDF flyer
37.0 MB
1.0 MB
1.0 MB
Mcule DEL Compatible BB Library Building blocks suitable for DNA-encoded library synthesis Feb. 17, 2024 597,762
PDF flyer
zip
1.0 MB
8.0 MB
Mcule DEL Compatible In stock BB Library In stock building blocks suitable for DNA-encoded library synthesis Feb. 17, 2024 149,604
PDF flyer
zip
1.0 MB
2.0 MB
Mcule CNS Targeting Library Compounds with favorable CNS MPO and BBB scores Feb. 17, 2024 8,297,509
PDF flyer
zip
1.0 MB
426.0 MB
Mcule Macrocycle Library Macrocycles Feb. 17, 2024 108,984
PDF flyer
SMILES (smi.gz)
1.0 MB
2.0 MB
Mcule Macrocycle In stock Library In stock Macrocycles Feb. 17, 2024 48,443
PDF flyer
SMILES (smi.gz)
1.0 MB
1.0 MB
Mcule Functional group Annotated Library Compounds labeled with the number of specific functional group occurrences Feb. 17, 2024 41,766,991
csv.gz
PDF flyer
641.0 MB
1.0 MB
Mcule Protected Building Block Library Building blocks possessing one or more protected functions Feb. 17, 2024 4,660,955
csv.gz
PDF flyer
71.0 MB
1.0 MB
Mcule Protected In stock Building Block Library In stock building blocks possessing one or more protected functions Feb. 17, 2024 619,711
csv.gz
PDF flyer
11.0 MB
1.0 MB
Mcule Covalent Library Covalent fragments and druglike compounds Feb. 17, 2024 829,232
PDF flyer
zip
1.0 MB
12.0 MB
Mcule Covalent In stock Library In stock covalent fragments and druglike compounds Feb. 17, 2024 144,026
PDF flyer
zip
1.0 MB
2.0 MB
Mcule Amino acid Library Amino acids for peptide synthesis Feb. 17, 2024 187,586
PDF flyer
zip
1.0 MB
2.0 MB
Mcule Amino acid In stock Library In stock amino acids for peptide synthesis Feb. 17, 2024 47,836
PDF flyer
zip
1.0 MB
1.0 MB
Mcule Nucleotide Library Nucleotide derivatives Feb. 17, 2024 126,225
PDF flyer
SMILES (smi.gz)
1.0 MB
1.0 MB
Mcule "Click" Library Azide and alkyne building blocks suitable for "click chemistry" Feb. 17, 2024 79,481
PDF flyer
zip
1.0 MB
1.0 MB
Mcule "Click" In stock Library Azide and alkyne in stock building blocks suitable for "click chemistry" Feb. 17, 2024 16,139
PDF flyer
zip
1.0 MB
1.0 MB
Mcule High Solubility Fragment Library Fragments with high experimental solubility Dec. 2, 2020 2,650
PDF flyer
2D SDF (sdf.gz)
1.0 MB
1.0 MB
Mcule Chemical Probes Portal subset Small molecule modulators with 3-4 star in-vitro/in-cell rating on the Chemical Probes Portal June 22, 2023 232
csv.gz
PDF flyer
1.0 MB
1.0 MB
Mcule BindingDB subset Compounds associated with experimental protein-small molecule interaction data from BindingDB June 22, 2023 65,210
csv.gz
PDF flyer
3.0 MB
1.0 MB

If you need the database in smaller chunks, please visit the documentation site where you can find detailed instructions on how to create smaller files.

Quality is important

The design of screening libraries and the development of predictive drug discovery models all start with a high quality database. Chemical correctness is crucial because mis-drawn and imperfectly defined structures result in incorrect models, misleading predictions and inconsistent hits. Problematic structures should therefore be eliminated at the earliest possible stage from a drug discovery pipeline.


Why the mcule database is of high quality

The mcule database is curated by MAC (mcule advanced curation) that involves a rigorous molecule registration system based on more than 80 structural checks, standardization, preparation and correction steps. MAC guarantees high quality search results and avoids common errors arising from mis-drawn and incorrect structures that can critically affect the quality of computational calculations and the efficiency of experimental results. Learn more about our MAC technology


Purchase compounds from mcule

The high quality mcule database ensures high quality hits for your research projects. We keep our database up-to-date. Stock availability for more than 90% of our products is instantly or daily updated. Our procurement service delivers compounds to almost anywhere in the world quickly and efficiently. No matter how many suppliers you have selected compounds from, we deliver them to your door as a single package. Single website, single contact, single package.

Our goal is to incorporate all purchasable compounds into the mcule database. Please send the name and website of your favourite chemical supplier that you would like to be added to the mcule high quality database.


How to purchase the selected compounds

After signing into your mcule account, paste or upload a list of mcule IDs into our Find Chemicals interface and click on "Search". Then click on the orange "Quote" button, fill out the quote form and submit your quote request. If you have access to Instant Quote, we will provide you with a quote on-the-fly, if not, you can choose Next-Day Quote and we will get back with a quotation in 24-48 hours.

Challenge us! If you have hits from other databases, you can upload them in SMILES, InChI or SDF formats, and see how many of them are purchasable from mcule.

Download or filter by supplier data

If you need more information such as stock availability and supplier names and IDs, subscribe to one of our plans.

Subscribed users can download supplier data for all purchasable compounds including supplier name and ID, catalog name, purity and stock availability. Moreover, you get access to the Product filter that conveniently selects any subset of the mcule database based on your criteria. Use the Product filter to design your own screening library!


Library design tools at mcule.com

Design special libraries, prepare custom subsets of the mcule database by using drug discovery tools at mcule.com. Select compounds online with molecular modeling and cheminformatic tools. Diversity selection, property filtering, similarity and substructure searching, molecular docking and more. Try the Workflow builder now.

Sign up for free


Download our brochure on Mcule Compound Sourcing

Download our Compound Sourcing User Guide

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