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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 Checksum
Mcule Full Purchasable Mcule supplier & ULTIMATE catalogs Aug. 15, 2025 44,067,277
2D SDF (sdf.gz)
SMILES (smi.gz)
9.8 GB
565.0 MB
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Mcule In Stock Purchasable Mcule supplier in stock catalogs Aug. 16, 2025 6,529,267
2D SDF (sdf.gz)
SMILES (smi.gz)
1.4 GB
96.0 MB
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Mcule Full Building Blocks Purchasable Mcule supplier building block catalogs Aug. 16, 2025 6,529,202
2D SDF (sdf.gz)
SMILES (smi.gz)
930.0 MB
85.0 MB
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Mcule Known Stock Amounts Purchasable Mcule supplier in stock catalogs with known stock amount Aug. 16, 2025 5,650,397
2D SDF (sdf.gz)
SMILES (smi.gz)
1.3 GB
84.0 MB
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Mcule Virtual Purchasable Mcule supplier virtual catalogs & ULTIMATE catalogs Aug. 16, 2025 37,354,056
2D SDF (sdf.gz)
SMILES (smi.gz)
8.3 GB
467.0 MB
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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
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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
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Mcule Express Building Blocks Pre-weighed Building Blocks stored at Mcule's EU hub. Dispatched within 24 hours. July 10, 2025 6,160
csv.gz
PDF flyer
1.0 MB
1.0 MB
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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 Checksum
Mcule Natural Products Library Natural products and derivatives from natural or synthetic sources in separate files Aug. 4, 2025 180,234
csv.gz
PDF flyer
9.0 MB
1.0 MB
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Mcule Natural Products in stock Library In stock natural products and derivatives from natural or synthetic sources in separate files Aug. 4, 2025 174,060
csv.gz
PDF flyer
9.0 MB
1.0 MB
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Mcule Unique BB Library Building blocks exclusively sourced from single suppliers Aug. 19, 2025 2,660,928
csv.gz
PDF flyer
41.0 MB
1.0 MB
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Mcule Unique In stock BB Library In stock building blocks exclusively sourced from single suppliers Aug. 19, 2025 135,364
csv.gz
PDF flyer
3.0 MB
1.0 MB
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Mcule Unique High Confidence BB Library Building blocks that are available from single suppliers only. This set of building blocks can be sourced with outstanding success rate and lead time. Aug. 19, 2025 135,364
csv.gz
PDF flyer
3.0 MB
1.0 MB
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Mcule Amidite Library Building blocks containing ribose and/or phosphoramidite patterns suitable for nucleotide synthesis Aug. 19, 2025 11,193
PDF flyer
zip
1.0 MB
1.0 MB
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Mcule Amidite In stock Library In stock building blocks containing ribose and/or phosphoramidite patterns suitable for nucleotide synthesis Aug. 19, 2025 6,532
PDF flyer
zip
1.0 MB
1.0 MB
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Mcule Unnatural Amino Acid Library Unnatural amino acids for peptide synthesis Aug. 19, 2025 70,826
PDF flyer
zip
1.0 MB
1.0 MB
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Mcule Unnatural Amino Acid In stock Library In stock unnatural amino acids for peptide synthesis Aug. 19, 2025 24,962
PDF flyer
zip
1.0 MB
1.0 MB
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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) Aug. 19, 2025 701,186
PDF flyer
zip
1.0 MB
66.0 MB
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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) Aug. 19, 2025 370,464
PDF flyer
zip
1.0 MB
40.0 MB
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Mcule Kinase Targeting Library Compounds showing high molecular similarity to known orthosteric protein kinase binders and their regulatory subunits. Aug. 19, 2025 30,982
csv.gz
PDF
PDF flyer
3.0 MB
1.0 MB
1.0 MB
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Mcule Kinase Targeting In stock Library In stock compounds showing high molecular similarity to known orthosteric protein kinase binders and their regulatory subunits. Aug. 19, 2025 4,599
csv.gz
PDF
PDF flyer
1.0 MB
1.0 MB
1.0 MB
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Mcule Bioactivity Library Phenotypic/Epigenetic/Chemogenomic screening of bioactive compounds with ChEMBL and GtoP annotations Aug. 19, 2025 35,411
PDF flyer
zip
1.0 MB
5.0 MB
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Mcule Bioactivity In stock Library Phenotypic/Epigenetic/Chemogenomic screening of bioactive in stock compounds with ChEMBL and GtoP annotations Aug. 19, 2025 26,421
PDF flyer
zip
1.0 MB
4.0 MB
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Mcule Bioactivity Economy In stock Library Phenotypic/Epigenetic/Chemogenomic screening of bioactive in stock, cost-effective compounds with ChEMBL and GtoP annotations Aug. 19, 2025 7,474
PDF flyer
zip
1.0 MB
1.0 MB
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Mcule Fragment Library Fragments Aug. 19, 2025 371,114
PDF flyer
zip
1.0 MB
4.0 MB
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Mcule In stock Fragment Library In stock fragments Aug. 19, 2025 184,271
PDF flyer
zip
1.0 MB
2.0 MB
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Mcule Economy In stock Fragment Library In stock, cost-effective fragments Aug. 19, 2025 10,059
PDF flyer
zip
1.0 MB
1.0 MB
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Mcule HTS Library ‘True Positive’ High Throughput Screening hits Aug. 19, 2025 1,772,233
PDF flyer
SMILES (smi.gz)
1.0 MB
22.0 MB
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Mcule In stock HTS Library ‘In stock True Positive’ High Throughput Screening hits Aug. 19, 2025 608,799
PDF flyer
SMILES (smi.gz)
1.0 MB
8.0 MB
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Mcule Molecular Glue Library Small molecules with mostly two binding sites, of which one is an E3 ligase binding substructure. Aug. 19, 2025 28,116
PDF flyer
SMILES (smi.gz)
1.0 MB
1.0 MB
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Mcule Molecular Glue In stock Library In stock small molecules with mostly two binding sites, of which one is an E3 ligase binding substructure. Aug. 19, 2025 8,573
PDF flyer
SMILES (smi.gz)
1.0 MB
1.0 MB
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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. Aug. 19, 2025 3,672
PDF flyer
SMILES (smi.gz)
1.0 MB
1.0 MB
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Mcule GPCR Targeting Library Compounds that are annotated with the GPCR receptor subfamilies they potentially target Aug. 19, 2025 3,740,682
csv.gz
PDF
PDF flyer
248.0 MB
1.0 MB
1.0 MB
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Mcule GPCR Targeting In stock Library In stock compounds that are annotated with the GPCR receptor subfamilies they potentially target Aug. 19, 2025 315,037
csv.gz
PDF
PDF flyer
19.0 MB
1.0 MB
1.0 MB
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Mcule DEL-Compatible BB Library Building blocks suitable for DNA-encoded library synthesis Aug. 19, 2025 274,356
PDF flyer
zip
1.0 MB
4.0 MB
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Mcule DEL-Compatible In stock BB Library In stock building blocks suitable for DNA-encoded library synthesis Aug. 19, 2025 82,983
PDF flyer
zip
1.0 MB
1.0 MB
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Mcule DEL-Compatible Economy In stock BB Library In stock, cheap building blocks suitable for DNA-encoded library synthesis Aug. 19, 2025 11,024
PDF flyer
zip
1.0 MB
1.0 MB
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Mcule CNS Targeting Libraries Two libraries containing compounds with favorable CNS MPO or BBB scores Aug. 19, 2025 8,836,628
PDF flyer
zip
1.0 MB
456.0 MB
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Mcule CNS Targeting In stock Libraries Two libraries containing in stock compounds with favorable CNS MPO or BBB scores Aug. 19, 2025 1,796,072
PDF flyer
zip
1.0 MB
103.0 MB
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Mcule CNS Targeting Economy In stock Libraries Two libraries containing in stock, cost-effective compounds with favorable CNS MPO or BBB scores Aug. 19, 2025 534,090
PDF flyer
zip
1.0 MB
27.0 MB
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Mcule Macrocycle Library Macrocycles Aug. 19, 2025 136,101
PDF flyer
SMILES (smi.gz)
1.0 MB
2.0 MB
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Mcule Macrocycle In stock Library In stock Macrocycles Aug. 19, 2025 62,776
PDF flyer
SMILES (smi.gz)
1.0 MB
1.0 MB
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Mcule Functional group Annotated Library Compounds labeled with the number of specific functional group occurrences Aug. 19, 2025 44,067,277
csv.gz
PDF flyer
663.0 MB
1.0 MB
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Mcule Functional group Annotated Building Block Library Building blocks labeled with the number of specific functional group occurrences June 21, 2025 6,511,831
csv.gz
PDF flyer
99.0 MB
1.0 MB
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Mcule Functional group Annotated In stock Building Block Library In stock building blocks labeled with the number of specific functional group occurrences June 21, 2025 2,059,837
csv.gz
PDF flyer
34.0 MB
1.0 MB
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Mcule Protected Building Block Library Building blocks possessing one or more protected functions Aug. 19, 2025 5,296,212
csv.gz
PDF flyer
83.0 MB
1.0 MB
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Mcule Protected In stock Building Block Library In stock building blocks possessing one or more protected functions Aug. 19, 2025 704,246
csv.gz
PDF flyer
13.0 MB
1.0 MB
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Mcule Covalent Library Covalent fragments and druglike compounds Aug. 19, 2025 934,836
PDF flyer
zip
1.0 MB
13.0 MB
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Mcule Covalent In stock Library In stock covalent fragments and druglike compounds Aug. 19, 2025 170,083
PDF flyer
zip
1.0 MB
3.0 MB
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Mcule Amino acid Library Amino acids for peptide synthesis Aug. 19, 2025 220,078
PDF flyer
zip
1.0 MB
3.0 MB
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Mcule Amino acid In stock Library In stock amino acids for peptide synthesis Aug. 19, 2025 52,770
PDF flyer
zip
1.0 MB
1.0 MB
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Mcule Agricultural Library Toxicologically favorable compounds with suitable properties for herbicide, fungicide, and insecticide discovery July 7, 2025 3,326,188
PDF flyer
zip
1.0 MB
70.0 MB
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Mcule Agricultural In stock Library Toxicologically favorable in stock compounds with suitable properties for herbicide, fungicide, and insecticide discovery July 7, 2025 900,511
PDF flyer
zip
1.0 MB
20.0 MB
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Mcule Nucleotide Base Library Compounds containing naturally occurring heteroaromatic bases Aug. 19, 2025 133,919
PDF flyer
SMILES (smi.gz)
1.0 MB
1.0 MB
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Mcule "Click" Library Azide and alkyne building blocks suitable for "click chemistry" Aug. 19, 2025 119,134
PDF flyer
zip
1.0 MB
1.0 MB
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Mcule "Click" In stock Library Azide and alkyne in stock building blocks suitable for "click chemistry" Aug. 19, 2025 20,375
PDF flyer
zip
1.0 MB
1.0 MB
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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
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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
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Mcule Chemical Probes Portal subset Small molecule modulators with 3-4 star in-vitro/in-cell rating on the Chemical Probes Portal March 8, 2025 648
csv.gz
PDF flyer
1.0 MB
1.0 MB
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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
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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 Compound Sourcing User Guide

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