MPD2   Click here for help

GtoPdb Ligand ID: 13349

Compound class: Synthetic organic
Comment: MPD2 is a PROTAC degrader of SARS-CoV-2 main protease (Mpro) [1]. It promotes cereblon (CRBN)-mediated, proteasome-driven degradation of the Mpro protein, and has anti-viral efficacy against a range of SARS-CoV-2 strains. Selective Mpro degradation is considered as an alternative pharmacological approach to small molecule inhibitors of protease activity.
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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
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 19
Hydrogen bond donors 5
Rotatable bonds 29
Topological polar surface area 253.94
Molecular weight 973.12
XLogP 3.88
No. Lipinski's rules broken 3

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 C[C@H]([C@@H](C(=O)N[C@@H](CC1CCCCC1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)C([H])=O)NC(=O)OCC3=CC=CC(=C3)OCCCCCCOC4=C5C(=CC=C4)C(=O)N(C6CCC(=O)NC6=O)C5=O)OC(C)(C)C
Isomeric SMILES O=C(N[C@@H](C[C@H]1C(NCC1)=O)C([H])=O)[C@H](CC2CCCCC2)NC([C@H]([C@@H](C)OC(C)(C)C)NC(OCC3=CC(OCCCCCCOC4=CC=CC=5C(N(C6CCC(NC6=O)=O)C(C54)=O)=O)=CC=C3)=O)=O
InChI InChI=1S/C51H68N6O13/c1-31(70-51(2,3)4)43(47(63)54-38(27-32-14-8-7-9-15-32)45(61)53-35(29-58)28-34-22-23-52-44(34)60)56-50(66)69-30-33-16-12-17-36(26-33)67-24-10-5-6-11-25-68-40-19-13-18-37-42(40)49(65)57(48(37)64)39-20-21-41(59)55-46(39)62/h12-13,16-19,26,29,31-32,34-35,38-39,43H,5-11,14-15,20-25,27-28,30H2,1-4H3,(H,52,60)(H,53,61)(H,54,63)(H,56,66)(H,55,59,62)/t31-,34+,35+,38+,39?,43+/m1/s1
InChI Key ZKSDAFLRLHGTNH-DTKLLKMQSA-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/)
References
1. Alugubelli YR, Xiao J, Khatua K, Kumar S, Sun L, Ma Y, Ma XR, Vulupala VR, Atla S, Blankenship LR et al.. (2024)
Discovery of First-in-Class PROTAC Degraders of SARS-CoV-2 Main Protease.
J Med Chem, 67 (8): 6495-6507. [PMID:38608245]
2. Cao W, Cho CD, Geng ZZ, Shaabani N, Ma XR, Vatansever EC, Alugubelli YR, Ma Y, Chaki SP, Ellenburg WH et al.. (2022)
Evaluation of SARS-CoV-2 Main Protease Inhibitors Using a Novel Cell-Based Assay.
ACS Cent Sci, 8 (2): 192-204. [PMID:35229034]
3. Yang KS, Ma XR, Ma Y, Alugubelli YR, Scott DA, Vatansever EC, Drelich AK, Sankaran B, Geng ZZ, Blankenship LR et al.. (2021)
A Quick Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors*.
ChemMedChem, 16 (6): 942-948. [PMID:33283984]