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 | March 8, 2025 | 43,897,561 |
2D SDF (sdf.gz)
SMILES (smi.gz)
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9.8 GB
563.0 MB
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SHA-256 checksum of mcule_purchasable_full_250308.smi.gz:
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| Mcule In Stock | Purchasable Mcule supplier in stock catalogs | March 9, 2025 | 6,317,976 |
2D SDF (sdf.gz)
SMILES (smi.gz)
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1.4 GB
93.0 MB
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SHA-256 checksum of mcule_purchasable_in_stock_250309.sdf.gz:
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SHA-256 checksum of mcule_purchasable_in_stock_250309.smi.gz:
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| Mcule Full Building Blocks | Purchasable Mcule supplier building block catalogs | March 9, 2025 | 6,404,175 |
2D SDF (sdf.gz)
SMILES (smi.gz)
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912.0 MB
83.0 MB
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SHA-256 checksum of mcule_purchasable_building_blocks_250309.sdf.gz:
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| Mcule Known Stock Amounts | Purchasable Mcule supplier in stock catalogs with known stock amount | March 9, 2025 | 5,359,936 |
2D SDF (sdf.gz)
SMILES (smi.gz)
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1.2 GB
80.0 MB
|
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SHA-256 checksum of mcule_purchasable_known_stock_amounts_250309.sdf.gz:
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| Mcule Virtual | Purchasable Mcule supplier virtual catalogs & ULTIMATE catalogs | March 9, 2025 | 37,387,423 |
2D SDF (sdf.gz)
SMILES (smi.gz)
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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)
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3.0 GB
186.0 MB
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SHA-256 checksum of mcule_ultimate_express_220828.sdf.gz:
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SHA-256 checksum of mcule_ultimate_express_220828.smi.gz:
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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)
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65.0 MB
6.0 MB
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SHA-256 checksum of mcule_ultimate_express1_220828.sdf.gz:
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SHA-256 checksum of mcule_ultimate_express1_220828.smi.gz:
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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 Unique BB Library | Building blocks exclusively sourced from single suppliers | March 8, 2025 | 2,600,874 |
csv.gz
PDF flyer
|
42.0 MB
1.0 MB
|
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SHA-256 checksum of mcule_unique_bb_library_250308.csv.gz:
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SHA-256 checksum of Mcule_Unique_Building_Block_Library_Flyer.pdf:
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| Mcule Unique In stock BB Library | In stock building blocks exclusively sourced from single suppliers | March 8, 2025 | 76,940 |
csv.gz
PDF flyer
|
2.0 MB
1.0 MB
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SHA-256 checksum of mcule_unique_bb_instock_library_250308.csv.gz:
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SHA-256 checksum of Mcule_Unique_Building_Block_Library_Flyer.pdf:
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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. | Jan. 1, 2025 | 1,062,841 |
csv.gz
PDF flyer
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21.0 MB
1.0 MB
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SHA-256 checksum of mcule_unique_bb_high_confidence_library_250101.csv.gz:
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SHA-256 checksum of Mcule_Unique_Building_Block_Library_Flyer.pdf:
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| Mcule Amidite Library | Building blocks containing ribose and/or phosphoramidite patterns suitable for nucleotide synthesis | March 8, 2025 | 26,410 |
PDF flyer
zip
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1.0 MB
1.0 MB
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SHA-256 checksum of Mcule_Amidite_Library_Flyer.pdf:
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SHA-256 checksum of mcule_amidite_library_250308.zip:
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| Mcule Amidite In stock Library | In stock building blocks containing ribose and/or phosphoramidite patterns suitable for nucleotide synthesis | March 8, 2025 | 15,994 |
PDF flyer
zip
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1.0 MB
1.0 MB
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SHA-256 checksum of Mcule_Amidite_Library_Flyer.pdf:
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SHA-256 checksum of mcule_amidite_instock_library_250308.zip:
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| Mcule Unnatural Amino Acid Library | Unnatural amino acids for peptide synthesis | March 8, 2025 | 68,665 |
PDF flyer
zip
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1.0 MB
1.0 MB
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SHA-256 checksum of mcule_unnatural_amino_acid_library_250308.zip:
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| Mcule Unnatural Amino Acid In stock Library | In stock unnatural amino acids for peptide synthesis | March 8, 2025 | 22,382 |
PDF flyer
zip
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1.0 MB
1.0 MB
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SHA-256 checksum of Mcule_Unnatural_Amino_Acid_Library_Flyer.pdf:
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SHA-256 checksum of mcule_unnatural_amino_acid_instock_library_250308.zip:
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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) | March 8, 2025 | 698,731 |
PDF flyer
zip
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1.0 MB
66.0 MB
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SHA-256 checksum of Mcule_RNA_binding_library_flyer.pdf:
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SHA-256 checksum of mcule_rna_binding_library_250308.zip:
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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) | March 8, 2025 | 367,101 |
PDF flyer
zip
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1.0 MB
40.0 MB
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SHA-256 checksum of mcule_rna_binding_instock_library_250308.zip:
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| Mcule Kinase Targeting Library | Compounds showing high molecular similarity to known orthosteric protein kinase binders and their regulatory subunits. | March 8, 2025 | 30,917 |
csv.gz
PDF
PDF flyer
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3.0 MB
1.0 MB
1.0 MB
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SHA-256 checksum of mcule_kinase_library_250308.csv.gz:
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SHA-256 checksum of mcule_kinase_documentation.pdf:
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SHA-256 checksum of Mcule_Kinase_Targeting_Library_Flyer.pdf:
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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. | March 8, 2025 | 4,513 |
csv.gz
PDF
PDF flyer
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1.0 MB
1.0 MB
1.0 MB
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SHA-256 checksum of mcule_kinase_instock_library_250308.csv.gz:
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| Mcule Bioactivity Library | Phenotypic/Epigenetic/Chemogenomic screening of bioactive compounds with ChEMBL and GtoP annotations | March 8, 2025 | 34,886 |
PDF flyer
zip
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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 | March 8, 2025 | 25,763 |
PDF flyer
zip
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1.0 MB
4.0 MB
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SHA-256 checksum of Mcule_Bioactivity_Library_Flyer.pdf:
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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 | March 8, 2025 | 7,498 |
PDF flyer
zip
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1.0 MB
1.0 MB
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SHA-256 checksum of Mcule_Bioactivity_Library_Flyer.pdf:
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SHA-256 checksum of mcule_bioactivity_economy_library_250308.zip:
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| Mcule Fragment Library | Fragments | March 8, 2025 | 356,858 |
PDF flyer
zip
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1.0 MB
4.0 MB
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SHA-256 checksum of Mcule_Fragment_Library.pdf:
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SHA-256 checksum of mcule_fragment_library_250308.zip:
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| Mcule In stock Fragment Library | In stock fragments | March 8, 2025 | 154,744 |
PDF flyer
zip
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1.0 MB
2.0 MB
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SHA-256 checksum of Mcule_Fragment_Library.pdf:
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SHA-256 checksum of mcule_fragment_instock_library_250308.zip:
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| Mcule Economy In stock Fragment Library | In stock, cost-effective fragments | March 8, 2025 | 10,063 |
PDF flyer
zip
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1.0 MB
1.0 MB
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| Mcule HTS Library | ‘True Positive’ High Throughput Screening hits | March 8, 2025 | 1,760,130 |
PDF flyer
SMILES (smi.gz)
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1.0 MB
22.0 MB
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SHA-256 checksum of Mcule_True_Positive_High_Throughput_Screening_Library_flyer.pdf:
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| Mcule In stock HTS Library | ‘In stock True Positive’ High Throughput Screening hits | March 8, 2025 | 596,822 |
PDF flyer
SMILES (smi.gz)
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1.0 MB
8.0 MB
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SHA-256 checksum of Mcule_True_Positive_High_Throughput_Screening_Library_flyer.pdf:
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SHA-256 checksum of mcule_HTS_instock_library_250308.smi.gz:
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| Mcule Molecular Glue Library | Small molecules with mostly two binding sites, of which one is an E3 ligase binding substructure. | March 8, 2025 | 26,768 |
PDF flyer
SMILES (smi.gz)
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1.0 MB
1.0 MB
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SHA-256 checksum of Mcule_Molecular_Glue_Library_Flyer.pdf:
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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. | March 8, 2025 | 8,472 |
PDF flyer
SMILES (smi.gz)
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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. | March 8, 2025 | 3,672 |
PDF flyer
SMILES (smi.gz)
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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 | March 8, 2025 | 3,816,014 |
csv.gz
PDF
PDF flyer
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254.0 MB
1.0 MB
1.0 MB
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SHA-256 checksum of mcule_GPCR_library_250308.csv.gz:
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SHA-256 checksum of mcule_gpcr_documentation.pdf:
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| Mcule GPCR Targeting In stock Library | In stock compounds that are annotated with the GPCR receptor subfamilies they potentially target | March 8, 2025 | 438,372 |
csv.gz
PDF
PDF flyer
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28.0 MB
1.0 MB
1.0 MB
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| Mcule DEL-Compatible BB Library | Building blocks suitable for DNA-encoded library synthesis | March 8, 2025 | 667,250 |
PDF flyer
zip
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1.0 MB
9.0 MB
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SHA-256 checksum of Mcule_DEL_Library_Flyer.pdf:
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| Mcule DEL-Compatible In stock BB Library | In stock building blocks suitable for DNA-encoded library synthesis | March 8, 2025 | 157,337 |
PDF flyer
zip
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1.0 MB
3.0 MB
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| Mcule DEL-Compatible Economy In stock BB Library | In stock, cheap building blocks suitable for DNA-encoded library synthesis | March 8, 2025 | 29,184 |
PDF flyer
zip
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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 | March 8, 2025 | 8,526,770 |
PDF flyer
zip
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1.0 MB
441.0 MB
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| Mcule CNS Targeting In stock Libraries | Two libraries containing in stock compounds with favorable CNS MPO or BBB scores | March 8, 2025 | 1,482,158 |
PDF flyer
zip
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1.0 MB
84.0 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 | March 8, 2025 | 467,910 |
PDF flyer
zip
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1.0 MB
24.0 MB
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SHA-256 checksum of Mcule_CNS_Targeting_Library_Flyer.pdf:
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SHA-256 checksum of mcule_CNS_economy_library_250308.zip:
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| Mcule Macrocycle Library | Macrocycles | March 8, 2025 | 133,125 |
PDF flyer
SMILES (smi.gz)
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1.0 MB
2.0 MB
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SHA-256 checksum of Mcule_macrocycles_library_flyer.pdf:
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| Mcule Macrocycle In stock Library | In stock Macrocycles | March 8, 2025 | 62,371 |
PDF flyer
SMILES (smi.gz)
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1.0 MB
1.0 MB
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SHA-256 checksum of Mcule_macrocycles_library_flyer.pdf:
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SHA-256 checksum of mcule_macrocycle_instock_library_250308.smi.gz:
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| Mcule Functional group Annotated Library | Compounds labeled with the number of specific functional group occurrences | March 8, 2025 | 43,897,561 |
csv.gz
PDF flyer
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711.0 MB
1.0 MB
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SHA-256 checksum of mcule_function_annotated_library_250308.csv.gz:
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| Mcule Protected Building Block Library | Building blocks possessing one or more protected functions | March 8, 2025 | 5,269,171 |
csv.gz
PDF flyer
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82.0 MB
1.0 MB
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SHA-256 checksum of mcule_pg_library_250308.csv.gz:
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SHA-256 checksum of Mcule_Protected_Building_Block_Library_Flyer.pdf:
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| Mcule Protected In stock Building Block Library | In stock building blocks possessing one or more protected functions | March 8, 2025 | 670,009 |
csv.gz
PDF flyer
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12.0 MB
1.0 MB
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SHA-256 checksum of mcule_pg_instock_library_250308.csv.gz:
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| Mcule Covalent Library | Covalent fragments and druglike compounds | March 8, 2025 | 945,685 |
PDF flyer
zip
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1.0 MB
14.0 MB
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| Mcule Covalent In stock Library | In stock covalent fragments and druglike compounds | March 8, 2025 | 160,684 |
PDF flyer
zip
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1.0 MB
3.0 MB
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SHA-256 checksum of Mcule_covalent_library_flyer.pdf:
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SHA-256 checksum of mcule_covalent_instock_library_250308.zip:
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| Mcule Amino acid Library | Amino acids for peptide synthesis | March 8, 2025 | 218,478 |
PDF flyer
zip
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1.0 MB
3.0 MB
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SHA-256 checksum of Mcule_amino_acid_library_flyer.pdf:
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| Mcule Amino acid In stock Library | In stock amino acids for peptide synthesis | March 8, 2025 | 50,014 |
PDF flyer
zip
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1.0 MB
1.0 MB
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| Mcule Nucleotide Base Library | Compounds containing naturally occurring heteroaromatic bases | March 8, 2025 | 133,135 |
PDF flyer
SMILES (smi.gz)
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1.0 MB
1.0 MB
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| Mcule "Click" Library | Azide and alkyne building blocks suitable for "click chemistry" | March 8, 2025 | 115,699 |
PDF flyer
zip
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1.0 MB
1.0 MB
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SHA-256 checksum of Mcule_Click_Library_Flyer.pdf:
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| Mcule "Click" In stock Library | Azide and alkyne in stock building blocks suitable for "click chemistry" | March 8, 2025 | 18,432 |
PDF flyer
zip
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1.0 MB
1.0 MB
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SHA-256 checksum of Mcule_Click_Library_Flyer.pdf:
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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)
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1.0 MB
6.0 MB
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SHA-256 checksum of mcule_high_solubility_fragment_library_240428.sdf.gz:
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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
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176.0 MB
1.0 MB
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SHA-256 checksum of mcule_in_stock_annotated_by_cortex_discovery_241002.csv.gz:
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SHA-256 checksum of Mcule_In_Stock_Cortex_Discovery_Flyer.pdf:
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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
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1.0 MB
1.0 MB
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SHA-256 checksum of Mcule_Chemical_Probes_DB_subset_flyer.pdf:
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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
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3.0 MB
1.0 MB
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SHA-256 checksum of mcule_binding_db_library_20230626.csv.gz:
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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.
