compound 7 [PMID: 31381331]   Click here for help

GtoPdb Ligand ID: 10450

Immunopharmacology Ligand
Compound class: Synthetic organic
Comment: Compound 7 selectively inhibits αVβ6 integrin-mediated cell adhesion [1]. It was discovered in a medicinal chemistry effort to rationally design improved therapeutics for idiopathic pulmonary fibrosis (IPF).
Docking studies indicate that compound 7 binds in a pocket formed at the interface of the α and β integrin subunits. Since compound 7 is selective for β6-containing αV integrins we have recorded the binding data against the various β subunits tested, to make comparisons clearer.
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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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Click here for structure editor
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 5
Hydrogen bond donors 1
Rotatable bonds 9
Topological polar surface area 82.35
Molecular weight 501.31
XLogP 3.25
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 [O-]C(=O)CC(c1cccc(c1)n1nc(cc1C)C)C[N+]1(C)CCC(C1)CCc1ccc2c(n1)NCCC2
Isomeric SMILES [O-]C(=O)C[C@@H](c1cccc(c1)n1nc(cc1C)C)C[N@@+]1(C)CC[C@H](C1)CCc1ccc2c(n1)NCCC2
InChI InChI=1S/C30H39N5O2/c1-21-16-22(2)34(33-21)28-8-4-6-25(17-28)26(18-29(36)37)20-35(3)15-13-23(19-35)9-11-27-12-10-24-7-5-14-31-30(24)32-27/h4,6,8,10,12,16-17,23,26H,5,7,9,11,13-15,18-20H2,1-3H3,(H-,31,32,36,37)/t23-,26-,35+/m1/s1
InChI Key BXOSGYRJKCYDLH-YAYCEGLDSA-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. Barrett TN, Taylor JA, Barker D, Procopiou PA, Thompson JDF, Barrett J, Le J, Lynn SM, Pogany P, Pratley C et al.. (2019)
Profile of a Highly Selective Quaternized Pyrrolidine Betaine αvβ6 Integrin Inhibitor-(3S)-3-(3-(3,5-Dimethyl-1H-pyrazol-1-yl)phenyl)-4-((1S and 1R,3R)-1-methyl-3-(2-(5,6,7,8-tetrahydro-1,8-naphthyridin-2-yl)ethyl)pyrrolidin-1-ium-1-yl)butanoate Synthesized by Stereoselective Methylation.
J Med Chem, 62 (16): 7543-7556. [PMID:31381331]
2. Cirkel GA, Kerklaan BM, Vanhoutte F, Van der Aa A, Lorenzon G, Namour F, Pujuguet P, Darquenne S, de Vos FY, Snijders TJ et al.. (2016)
A dose escalating phase I study of GLPG0187, a broad spectrum integrin receptor antagonist, in adult patients with progressive high-grade glioma and other advanced solid malignancies.
Invest New Drugs, 34 (2): 184-92. [PMID:26792581]
3. Hatley RJD, Macdonald SJF, Slack RJ, Le J, Ludbrook SB, Lukey PT. (2018)
An αv-RGD Integrin Inhibitor Toolbox: Drug Discovery Insight, Challenges and Opportunities.
Angew Chem Int Ed Engl, 57 (13): 3298-3321. [PMID:28944552]
4. Kapp TG, Rechenmacher F, Neubauer S, Maltsev OV, Cavalcanti-Adam EA, Zarka R, Reuning U, Notni J, Wester HJ, Mas-Moruno C et al.. (2017)
A Comprehensive Evaluation of the Activity and Selectivity Profile of Ligands for RGD-binding Integrins.
Sci Rep, 7: 39805. [PMID:28074920]
5. Miller LM, Pritchard JM, Macdonald SJF, Jamieson C, Watson AJB. (2017)
Emergence of Small-Molecule Non-RGD-Mimetic Inhibitors for RGD Integrins.
J Med Chem, 60 (8): 3241-3251. [PMID:28135089]
6. Sheldrake HM, Patterson LH. (2014)
Strategies to inhibit tumor associated integrin receptors: rationale for dual and multi-antagonists.
J Med Chem, 57 (15): 6301-15. [PMID:24568695]