Loading ...

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:

Collection name Description Last updated Nb. of compounds Filetype Filesize Download
Mcule Purchasable (full) All purchasable, in stock & virtual compounds Sept. 18, 2017 35,772,718
2D SDF (sdf.gz)
SMILES (smi.gz)
5.6 GB
462.0 MB
Mcule Purchasable (in stock) All purchasable, in stock compounds Sept. 18, 2017 5,648,837
2D SDF (sdf.gz)
SMILES (smi.gz)
1.3 GB
84.0 MB
Mcule Purchasable (known stock amounts) All purchasable, in stock compounds with known exact stock amount Sept. 18, 2017 4,721,686
2D SDF (sdf.gz)
SMILES (smi.gz)
1.1 GB
70.0 MB
Mcule Purchasable (instant quotable) All purchasable compounds with known prices Sept. 18, 2017 35,638,322
2D SDF (sdf.gz)
SMILES (smi.gz)
5.6 GB
460.0 MB
Mcule Purchasable (In Stock Ro5) Purchasable, in stock compounds filtered by rule-of-5 (max 1 violation) Feb. 11, 2017 5,469,303
2D SDF (sdf.gz)
SMILES (smi.gz)
1.2 GB
83.0 MB
Mcule Purchasable (In Stock Ro5 Diverse 1M) 1 million diverse, purchasable, in stock compounds filtered by rule-of-5 (max 1 violation) Dec. 8, 2016 1,000,000
2D SDF (sdf.gz)
SMILES (smi.gz)
288.0 MB
21.0 MB
Mcule Purchasable (In Stock Ro5 Diverse 350K) 350,000 diverse, purchasable, in stock compounds filtered by rule-of-5 (max 1 violation) Dec. 8, 2016 350,000
2D SDF (sdf.gz)
SMILES (smi.gz)
101.0 MB
8.0 MB
Mcule Purchasable (In Stock & Virtual Ro5) Purchasable, in stock and virtual compounds filtered by rule-of-5 (max 1 violation) Feb. 11, 2017 35,173,992
SMILES (smi.gz)
496.0 MB
Mcule Purchasable (In Stock & Virtual Ro5 Diverse 2M) 2 million diverse, purchasable, in stock and virtual compounds filtered by rule-of-5 (max 1 violation) Feb. 11, 2017 2,000,000
2D SDF (sdf.gz)
SMILES (smi.gz)
480.0 MB
40.0 MB
Mcule Purchasable (In Stock & Virtual Ro5 Diverse 450k) 450,000 diverse, purchasable, in stock and virtual compounds filtered by rule-of-5 (max 1 violation) Feb. 11, 2017 450,000
2D SDF (sdf.gz)
SMILES (smi.gz)
110.0 MB
9.0 MB
Mcule Purchasable (In Stock Ro3) Purchasable, in stock compounds filtered by rule-of-3 (max 1 violation) Dec. 8, 2016 154,238
2D SDF (sdf.gz)
SMILES (smi.gz)
28.0 MB
3.0 MB
Mcule Purchasable (In Stock Ro3 Diverse 50K) 50,000 diverse, purchasable, in stock compounds filtered by rule-of-3 (max 1 violation) Dec. 8, 2016 50,000
2D SDF (sdf.gz)
SMILES (smi.gz)
90.0 MB
1.0 MB
Mcule Purchasable (In Stock & Virtual Ro3) Purchasable, in stock and virtual compounds filtered by rule-of-3 (max 1 violation) Dec. 8, 2016 789,907
2D SDF (sdf.gz)
SMILES (smi.gz)
123.0 MB
13.0 MB
Mcule Purchasable (In Stock & Virtual Ro3 Diverse 70K) 70,000 diverse, purchasable, in stock and virtual compounds filtered by rule-of-3 (max 1 violation) Dec. 8, 2016 70,000
2D SDF (sdf.gz)
SMILES (smi.gz)
12.0 MB
1.0 MB

If you need the database in any other format or in smaller chunks, please don't hesitate to contact us at [javascript protected email address].

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, FTrees Visual Similarities and more. Try the Workflow builder now.

Sign up for free


Download our brochure on Mcule Compound Sourcing

Download our Compound Sourcing User Guide

loader