SP-4206   Click here for help

GtoPdb Ligand ID: 9037

Synonyms: compound 13 [PMID:12656598] | SP4206 [3]
PDB Ligand Immunopharmacology Ligand
Compound class: Synthetic organic
Comment: SP-4206 is a small molecule protein-protein interaction inhibitor. It binds IL-2 and prevents its interaction with the IL-2 receptor α [1-2]. The X-ray structure of SP-4206 bound to a dynamic hot spot on IL-2 is presented with PDB identifier 1PY2 [4].

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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 10
Hydrogen bond donors 4
Rotatable bonds 14
Topological polar surface area 191.3
Molecular weight 661.22
XLogP 3.25
No. Lipinski's rules broken 1

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(CC(C(=O)NCC(=O)N1CCC(CC1)c1cc(nn1C)c1ccc(c(c1Cl)Cl)OCc1ccc(o1)C(=O)O)N=C(N)N)C
Isomeric SMILES CC(C[C@H](C(=O)NCC(=O)N1CCC(CC1)c1cc(nn1C)c1ccc(c(c1Cl)Cl)OCc1ccc(o1)C(=O)O)N=C(N)N)C
InChI InChI=1S/C30H37Cl2N7O6/c1-16(2)12-21(36-30(33)34)28(41)35-14-25(40)39-10-8-17(9-11-39)22-13-20(37-38(22)3)19-5-7-23(27(32)26(19)31)44-15-18-4-6-24(45-18)29(42)43/h4-7,13,16-17,21H,8-12,14-15H2,1-3H3,(H,35,41)(H,42,43)(H4,33,34,36)/t21-/m1/s1
InChI Key VNZHOIDQBPFEJU-OAQYLSRUSA-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. Arkin MR, Wells JA. (2004)
Small-molecule inhibitors of protein-protein interactions: progressing towards the dream.
Nat Rev Drug Discov, 3 (4): 301-17. [PMID:15060526]
2. Braisted AC, Oslob JD, Delano WL, Hyde J, McDowell RS, Waal N, Yu C, Arkin MR, Raimundo BC. (2003)
Discovery of a potent small molecule IL-2 inhibitor through fragment assembly.
J Am Chem Soc, 125 (13): 3714-5. [PMID:12656598]
3. Thanos CD, DeLano WL, Wells JA. (2006)
Hot-spot mimicry of a cytokine receptor by a small molecule.
Proc Natl Acad Sci USA, 103 (42): 15422-7. [PMID:17032757]
4. Thanos CD, Randal M, Wells JA. (2003)
Potent small-molecule binding to a dynamic hot spot on IL-2.
J Am Chem Soc, 125 (50): 15280-1. [PMID:14664558]