nirmatrelvir   Click here for help

GtoPdb Ligand ID: 11503

Synonyms: example E61 [WO2021250648A1] | Paxlovid® (nirmatrelvir + ritonavir) | PF-07321332 | PF07321332
Approved drug PDB Ligand
nirmatrelvir is an approved drug (UK MHRA (2021), EMA (2022), FDA (2023))
Compound class: Synthetic organic
Comment: PF-07321332 (nirmatrelvir) is an oral antiviral clinical lead. It is a covalent inhibitor of SARS-CoV-2 Mpro (main protease, 3CLpro) that binds to cysteine145 within the enzyme's catalytic domain [4-5]. Mpro is essential for coronavirus replication. Inhibiting Mpro actvity blocks replication at an early stage in the virus' life cycle. Due to structural similarities between the Mpro's of other coronavirusus, PF-07321332 offers the potential of pan-coronavirus activity. In vitro it is suggested to inhibit replication of CoV-2 variants including delta and omicron.

PF-07321332 is structurally similar to ML1000. Prior to peer-reviewed name-to-structure disclosure, we obtained the structure represented here from an online report by Dr Bethany Halford who attended a session by Dafydd Owen (Pfizer) at the ACS Spring 2021 meeting (@beth_halford image on Twitter) which rendered the SMILES string N#C[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H]1N(C[C@H]2[C@@H]1C2(C)C)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F. PF-07321332's chemical structure was formally disclosed in Owen et al's Science article in November 2021 [3], and this confirmed the structure that was obtained during the ACS meeting.
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Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

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View interactive charts of activity data across species

nirmatrelvir is commercially available from our sponsors

2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 9
Hydrogen bond donors 3
Rotatable bonds 11
Topological polar surface area 131.4
Molecular weight 499.24
XLogP 1.39
No. Lipinski's rules broken 0

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES N#C[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H]1N(C[C@H]2[C@@H]1C2(C)C)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F
Isomeric SMILES N#C[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H]1N(C[C@H]2[C@@H]1C2(C)C)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F
InChI InChI=1S/C23H32F3N5O4/c1-21(2,3)16(30-20(35)23(24,25)26)19(34)31-10-13-14(22(13,4)5)15(31)18(33)29-12(9-27)8-11-6-7-28-17(11)32/h11-16H,6-8,10H2,1-5H3,(H,28,32)(H,29,33)(H,30,35)/t11-,12-,13-,14-,15-,16+/m0/s1
InChI Key LIENCHBZNNMNKG-OJFNHCPVSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
Classification Click here for help
Compound class Synthetic organic
Approved drug? Yes. UK MHRA (2021)  |  EMA (2022)  |  FDA (2023)
IUPAC Name Click here for help
(1R,2S,5S)-N-[(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl]-3-[(2S)-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide
International Nonproprietary Names Click here for help
INN number INN
12161 nirmatrelvir
Synonyms Click here for help
example E61 [WO2021250648A1] | Paxlovid® (nirmatrelvir + ritonavir) | PF-07321332 | PF07321332
Database Links Click here for help
CAS Registry No. 2628280-40-8 (source: PubChem)
GtoPdb PubChem SID 441604875
PubChem CID 155903259
RCSB PDB Ligand ZGW
Search Google for chemical match using the InChIKey LIENCHBZNNMNKG-OJFNHCPVSA-N
Search Google for chemicals with the same backbone LIENCHBZNNMNKG
Search PubMed clinical trials nirmatrelvir
Search PubMed titles nirmatrelvir
Search PubMed titles/abstracts nirmatrelvir
UniChem Compound Search for chemical match using the InChIKey LIENCHBZNNMNKG-OJFNHCPVSA-N
UniChem Connectivity Search for chemical match using the InChIKey LIENCHBZNNMNKG-OJFNHCPVSA-N

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MedChemExpress
Nirmatrelvir (links to external site)
Cat. No. HY-138687