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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 June 10, 2024 42,114,386
2D SDF (sdf.gz)
SMILES (smi.gz)
9.5 GB
535.0 MB
Mcule In Stock Purchasable Mcule supplier in stock catalogs June 10, 2024 5,883,774
2D SDF (sdf.gz)
SMILES (smi.gz)
1.3 GB
87.0 MB
Mcule Full Building Blocks Purchasable Mcule supplier building block catalogs June 10, 2024 4,790,835
2D SDF (sdf.gz)
SMILES (smi.gz)
651.0 MB
59.0 MB
Mcule Known Stock Amounts Purchasable Mcule supplier in stock catalogs with known stock amount June 10, 2024 5,090,951
2D SDF (sdf.gz)
SMILES (smi.gz)
1.2 GB
76.0 MB
Mcule Virtual Purchasable Mcule supplier virtual catalogs & ULTIMATE catalogs June 10, 2024 35,990,948
2D SDF (sdf.gz)
SMILES (smi.gz)
8.1 GB
446.0 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) June 18, 2024 684,218
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) June 18, 2024 357,429
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. June 18, 2024 29,661
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. June 18, 2024 3,546
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 June 18, 2024 33,075
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 annotations June 18, 2024 25,010
PDF flyer
zip
1.0 MB
4.0 MB
Mcule Bioactivity Economy In stock Library Phenotypic/Epigenetic/Chemogenomic screening of bioactive in stock, cheap compounds with ChEMBL annotations June 18, 2024 9,073
PDF flyer
zip
1.0 MB
1.0 MB
Mcule Fragment Library Fragments June 18, 2024 307,011
PDF flyer
zip
1.0 MB
4.0 MB
Mcule In stock Fragment Library In stock fragments June 18, 2024 144,335
PDF flyer
zip
1.0 MB
2.0 MB
Mcule Economy In stock Fragment Library In stock, cheap fragments June 18, 2024 9,764
PDF flyer
zip
1.0 MB
1.0 MB
Mcule HTS Library ‘True Positive’ High Throughput Screening hits June 18, 2024 1,624,836
PDF flyer
SMILES (smi.gz)
1.0 MB
20.0 MB
Mcule In stock HTS Library ‘In stock True Positive’ High Throughput Screening hits June 18, 2024 498,242
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 an E3 ligase binding substructure. June 18, 2024 25,808
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. June 18, 2024 8,116
PDF flyer
SMILES (smi.gz)
1.0 MB
1.0 MB
Mcule Molecular Glue Economy In stock Library In stock, cheap small molecules with mostly two binding sites, of which one is an E3 ligase binding substructure. June 18, 2024 4,578
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 June 18, 2024 3,658,525
csv.gz
PDF
PDF flyer
245.0 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 June 18, 2024 380,392
csv.gz
PDF
PDF flyer
24.0 MB
1.0 MB
1.0 MB
Mcule DEL-Compatible BB Library Building blocks suitable for DNA-encoded library synthesis June 18, 2024 608,975
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 June 18, 2024 144,900
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 June 18, 2024 29,425
PDF flyer
zip
1.0 MB
1.0 MB
Mcule CNS Targeting Library Compounds with favorable CNS MPO and BBB scores June 18, 2024 8,274,640
PDF flyer
zip
1.0 MB
426.0 MB
Mcule CNS Targeting In stock Library In stock compounds with favorable CNS MPO and BBB scores June 18, 2024 1,452,477
PDF flyer
zip
1.0 MB
86.0 MB
Mcule CNS Targeting Economy In stock Library In stock, cheap compounds with favorable CNS MPO and BBB scores June 18, 2024 473,782
PDF flyer
zip
1.0 MB
25.0 MB
Mcule Macrocycle Library Macrocycles June 18, 2024 113,741
PDF flyer
SMILES (smi.gz)
1.0 MB
2.0 MB
Mcule Macrocycle In stock Library In stock Macrocycles June 18, 2024 48,815
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 June 18, 2024 42,114,386
csv.gz
PDF flyer
646.0 MB
1.0 MB
Mcule Protected Building Block Library Building blocks possessing one or more protected functions June 18, 2024 4,745,484
csv.gz
PDF flyer
72.0 MB
1.0 MB
Mcule Protected In stock Building Block Library In stock building blocks possessing one or more protected functions June 18, 2024 627,323
csv.gz
PDF flyer
11.0 MB
1.0 MB
Mcule Covalent Library Covalent fragments and druglike compounds June 18, 2024 857,201
PDF flyer
zip
1.0 MB
12.0 MB
Mcule Covalent In stock Library In stock covalent fragments and druglike compounds June 18, 2024 141,196
PDF flyer
zip
1.0 MB
2.0 MB
Mcule Amino acid Library Amino acids for peptide synthesis June 18, 2024 188,677
PDF flyer
zip
1.0 MB
2.0 MB
Mcule Amino acid In stock Library In stock amino acids for peptide synthesis June 18, 2024 48,770
PDF flyer
zip
1.0 MB
1.0 MB
Mcule Nucleotide Library Nucleotide derivatives June 18, 2024 112,677
PDF flyer
SMILES (smi.gz)
1.0 MB
1.0 MB
Mcule "Click" Library Azide and alkyne building blocks suitable for "click chemistry" June 18, 2024 94,690
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" June 18, 2024 16,678
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
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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