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].
Click here for help

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.

✖

View interactive charts of activity data across species
2D Structure
Click here for help

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.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. 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.

✖
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
SMILES / InChI / InChIKey
Click here for help

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.

✖
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
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]