peptide 22d   Click here for help

GtoPdb Ligand ID: 12063

Compound class: Synthetic organic
Comment: This is a macrocyclic peptide that targets the STUB1 E3 ubiquitin ligase [1]. 22d was developed from a short linear peptide (LWWPD) that binds STUB1 [2], to guide the design of more selective pharmacological inhibitors as tool compounds for target validation. Although 22d retains the binding affinity for STUB1 of the linear peptide, suboptimal cellular permeability means that this construct is not suitable for experiments in cells or in vivo.
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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 18
Hydrogen bond donors 9
Rotatable bonds 13
Topological polar surface area 333.91
Molecular weight 930.42
XLogP 3.54
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 CC[C@@H]([C@@H]1NC(=O)[C@H](CO)NC(=O)CCCOc2ccccc2CCSC[C@H](NC(=O)[C@@H](NC1=O)Cc1c[nH]c2c1cccc2)C(=O)N1CCC[C@H]1C(=O)N[C@H](C(=O)N)Cc1nnn[nH]1)C
Isomeric SMILES OC[C@H]1C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N2[C@H](C(=O)N[C@@H](Cc3nnn[nH]3)C(=O)N)CCC2)CSCCc2ccccc2OCCCC(=O)N1)Cc1c[nH]c2c1cccc2)[C@@H](C)CC
InChI InChI=1S/C44H58N12O9S/c1-3-25(2)38-43(63)49-31(20-27-22-46-29-12-6-5-11-28(27)29)40(60)50-33(44(64)56-17-8-13-34(56)42(62)48-30(39(45)59)21-36-52-54-55-53-36)24-66-19-16-26-10-4-7-14-35(26)65-18-9-15-37(58)47-32(23-57)41(61)51-38/h4-7,10-12,14,22,25,30-34,38,46,57H,3,8-9,13,15-21,23-24H2,1-2H3,(H2,45,59)(H,47,58)(H,48,62)(H,49,63)(H,50,60)(H,51,61)(H,52,53,54,55)/t25-,30-,31-,32-,33-,34-,38-/m0/s1
InChI Key CPNJMMBLVDNJTP-GQUKTMJCSA-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. Ng S, Brueckner AC, Bahmanjah S, Deng Q, Johnston JM, Ge L, Duggal R, Habulihaz B, Barlock B, Ha S et al.. (2022)
Discovery and Structure-Based Design of Macrocyclic Peptides Targeting STUB1.
J Med Chem, [Epub ahead of print]. [PMID:35853179]
2. Ravalin M, Theofilas P, Basu K, Opoku-Nsiah KA, Assimon VA, Medina-Cleghorn D, Chen YF, Bohn MF, Arkin M, Grinberg LT et al.. (2019)
Specificity for latent C termini links the E3 ubiquitin ligase CHIP to caspases.
Nat Chem Biol, 15 (8): 786-794. [PMID:31320752]