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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 Nov. 1, 2024 43,580,778
2D SDF (sdf.gz)
SMILES (smi.gz)
9.7 GB
559.0 MB
Mcule In Stock Purchasable Mcule supplier in stock catalogs Nov. 1, 2024 6,155,505
2D SDF (sdf.gz)
SMILES (smi.gz)
1.4 GB
91.0 MB
Mcule Full Building Blocks Purchasable Mcule supplier building block catalogs Nov. 2, 2024 6,164,972
2D SDF (sdf.gz)
SMILES (smi.gz)
876.0 MB
81.0 MB
Mcule Known Stock Amounts Purchasable Mcule supplier in stock catalogs with known stock amount Nov. 2, 2024 5,226,066
2D SDF (sdf.gz)
SMILES (smi.gz)
1.2 GB
78.0 MB
Mcule Virtual Purchasable Mcule supplier virtual catalogs & ULTIMATE catalogs Nov. 1, 2024 37,233,180
2D SDF (sdf.gz)
SMILES (smi.gz)
8.3 GB
466.0 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 Amidite Library Building blocks containing ribose and/or phosphoramidite patterns suitable for nucleotide synthesis Nov. 1, 2024 10,173
PDF flyer
zip
1.0 MB
1.0 MB
Mcule Amidite In stock Library In stock building blocks containing ribose and/or phosphoramidite patterns suitable for nucleotide synthesis Nov. 1, 2024 5,821
PDF flyer
zip
1.0 MB
1.0 MB
Mcule Unnatural Amino Acid Library Unnatural amino acids for peptide synthesis Nov. 1, 2024 67,873
PDF flyer
zip
1.0 MB
1.0 MB
Mcule Unnatural Amino Acid In stock Library In stock unnatural amino acids for peptide synthesis Nov. 1, 2024 21,958
PDF flyer
zip
1.0 MB
1.0 MB
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) Nov. 1, 2024 697,510
PDF flyer
zip
1.0 MB
66.0 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) Nov. 1, 2024 364,562
PDF flyer
zip
1.0 MB
40.0 MB
Mcule Kinase Targeting Library Compounds showing high molecular similarity to known orthosteric protein kinase binders and their regulatory subunits. Nov. 1, 2024 30,050
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. Nov. 1, 2024 3,627
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 and GtoP annotations Nov. 1, 2024 34,687
PDF flyer
zip
1.0 MB
5.0 MB
Mcule Bioactivity In stock Library Phenotypic/Epigenetic/Chemogenomic screening of bioactive in stock compounds with ChEMBL and GtoP annotations Nov. 1, 2024 25,557
PDF flyer
zip
1.0 MB
4.0 MB
Mcule Bioactivity Economy In stock Library Phenotypic/Epigenetic/Chemogenomic screening of bioactive in stock, cost-effective compounds with ChEMBL and GtoP annotations Nov. 1, 2024 7,650
PDF flyer
zip
1.0 MB
1.0 MB
Mcule Fragment Library Fragments Nov. 1, 2024 345,042
PDF flyer
zip
1.0 MB
4.0 MB
Mcule In stock Fragment Library In stock fragments Nov. 1, 2024 146,843
PDF flyer
zip
1.0 MB
2.0 MB
Mcule Economy In stock Fragment Library In stock, cost-effective fragments Nov. 1, 2024 9,020
PDF flyer
zip
1.0 MB
1.0 MB
Mcule HTS Library ‘True Positive’ High Throughput Screening hits Nov. 1, 2024 1,713,340
PDF flyer
SMILES (smi.gz)
1.0 MB
21.0 MB
Mcule In stock HTS Library ‘In stock True Positive’ High Throughput Screening hits Nov. 1, 2024 541,162
PDF flyer
SMILES (smi.gz)
1.0 MB
8.0 MB
Mcule Molecular Glue Library Small molecules with mostly two binding sites, of which one is an E3 ligase binding substructure. Nov. 1, 2024 26,627
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 an E3 ligase binding substructure. Nov. 1, 2024 8,395
PDF flyer
SMILES (smi.gz)
1.0 MB
1.0 MB
Mcule Molecular Glue Economy In stock Library In stock, cost-effective small molecules with mostly two binding sites, of which one is an E3 ligase binding substructure. Nov. 1, 2024 2,635
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 Nov. 1, 2024 3,587,978
csv.gz
PDF
PDF flyer
240.0 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 Nov. 1, 2024 396,583
csv.gz
PDF
PDF flyer
25.0 MB
1.0 MB
1.0 MB
Mcule DEL-Compatible BB Library Building blocks suitable for DNA-encoded library synthesis Nov. 1, 2024 653,911
PDF flyer
zip
1.0 MB
9.0 MB
Mcule DEL-Compatible In stock BB Library In stock building blocks suitable for DNA-encoded library synthesis Nov. 1, 2024 149,467
PDF flyer
zip
1.0 MB
2.0 MB
Mcule DEL-Compatible Economy In stock BB Library In stock, cheap building blocks suitable for DNA-encoded library synthesis Nov. 1, 2024 25,297
PDF flyer
zip
1.0 MB
1.0 MB
Mcule CNS Targeting Libraries Two libraries containing compounds with favorable CNS MPO or BBB scores Nov. 1, 2024 8,463,141
PDF flyer
zip
1.0 MB
444.0 MB
Mcule CNS Targeting In stock Libraries Two libraries containing in stock compounds with favorable CNS MPO or BBB scores Nov. 1, 2024 1,394,024
PDF flyer
zip
1.0 MB
88.0 MB
Mcule CNS Targeting Economy In stock Libraries Two libraries containing in stock, cost-effective compounds with favorable CNS MPO or BBB scores Nov. 1, 2024 260,104
PDF flyer
zip
1.0 MB
13.0 MB
Mcule Macrocycle Library Macrocycles Nov. 1, 2024 124,472
PDF flyer
SMILES (smi.gz)
1.0 MB
2.0 MB
Mcule Macrocycle In stock Library In stock Macrocycles Nov. 1, 2024 49,269
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 Nov. 1, 2024 43,580,778
csv.gz
PDF flyer
656.0 MB
1.0 MB
Mcule Protected Building Block Library Building blocks possessing one or more protected functions Nov. 1, 2024 5,227,654
csv.gz
PDF flyer
81.0 MB
1.0 MB
Mcule Protected In stock Building Block Library In stock building blocks possessing one or more protected functions Nov. 1, 2024 655,771
csv.gz
PDF flyer
12.0 MB
1.0 MB
Mcule Covalent Library Covalent fragments and druglike compounds Nov. 1, 2024 928,270
PDF flyer
zip
1.0 MB
13.0 MB
Mcule Covalent In stock Library In stock covalent fragments and druglike compounds Nov. 1, 2024 147,470
PDF flyer
zip
1.0 MB
2.0 MB
Mcule Amino acid Library Amino acids for peptide synthesis Nov. 1, 2024 216,776
PDF flyer
zip
1.0 MB
3.0 MB
Mcule Amino acid In stock Library In stock amino acids for peptide synthesis Nov. 1, 2024 50,111
PDF flyer
zip
1.0 MB
1.0 MB
Mcule Nucleotide Base Library Compounds containing naturally occurring heteroaromatic bases Nov. 1, 2024 116,734
PDF flyer
SMILES (smi.gz)
1.0 MB
1.0 MB
Mcule "Click" Library Azide and alkyne building blocks suitable for "click chemistry" Nov. 1, 2024 113,933
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" Nov. 1, 2024 18,044
PDF flyer
zip
1.0 MB
1.0 MB
Mcule High Solubility Fragment Library Fragments with high experimental solubility June 11, 2024 26,580
PDF flyer
2D SDF (sdf.gz)
1.0 MB
6.0 MB
Annotated Mcule In Stock Database In stock compounds annotated with advanced pharmacological properties generated by Cortex Discovery Oct. 2, 2024 5,943,993
csv.gz
PDF flyer
176.0 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.

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Download our Compound Sourcing User Guide

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