Ganglioside GD2   Click here for help

GtoPdb Ligand ID: 11342

Compound class: Synthetic organic
Comment: Ganglioside GD2 is a disialoganglioside cell adhesion molecule that is expressed on tumours of neuroectodermal origin, but which has restricted presence on normal cells. It is a drug target for neuroectoderm-derived tumours and sarcomas, including neuroblastoma, retinoblastoma, melanoma and small cell lung cancer [3]. Two monoclonal antibodies that target GD2 have been approved for clinical use in patients with high risk neuroblastoma: dinutuximab (2015) and naxitamab (2020). Both of these mAbs stimulate antibody-dependent cell-mediated cytotoxicity (ADCC) against GD2-expressing tumour cells.
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 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.

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Hydrogen bond acceptors 36
Hydrogen bond donors 22
Rotatable bonds 56
Topological polar surface area 600.82
Molecular weight 1590.9
XLogP 4.26
No. Lipinski's rules broken 3
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.

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Canonical SMILES CCCCCCCCCCCCC/C=C/C(C(NC(=O)CCCCCCCCCCCCCCCCC)CO[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O[C@@H]1O[C@H](CO)[C@@H]([C@@H]([C@H]1O)O[C@@]1(C[C@@H](O)[C@@H]([C@H](O1)C(C(CO[C@@]1(C[C@@H](O)[C@@H]([C@H](O1)C(C(CO)O)O)N)C(=O)O)O)O)N)C(=O)O)O[C@@H]1O[C@H](CO)[C@@H]([C@@H]([C@H]1NC(=O)C)O)O)O
Isomeric SMILES CCCCCCCCCCCCC/C=C/C(C(NC(=O)CCCCCCCCCCCCCCCCC)CO[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O[C@@H]1O[C@H](CO)[C@@H]([C@@H]([C@H]1O)O[C@@]1(C[C@@H](O)[C@@H]([C@H](O1)C(C(CO[C@@]1(C[C@@H](O)[C@@H]([C@H](O1)C(C(CO)O)O)N)C(=O)O)O)O)N)C(=O)O)O[C@@H]1O[C@H](CO)[C@@H]([C@@H]([C@H]1NC(=O)C)O)O)O
InChI InChI=1S/C74H134N4O32/c1-4-6-8-10-12-14-16-18-19-21-23-25-27-29-31-33-52(89)78-43(44(84)32-30-28-26-24-22-20-17-15-13-11-9-7-5-2)40-101-69-61(95)60(94)63(50(38-81)104-69)106-70-62(96)67(64(51(39-82)105-70)107-68-55(77-42(3)83)59(93)58(92)49(37-80)103-68)110-74(72(99)100)35-46(86)54(76)66(109-74)57(91)48(88)41-102-73(71(97)98)34-45(85)53(75)65(108-73)56(90)47(87)36-79/h30,32,43-51,53-70,79-82,84-88,90-96H,4-29,31,33-41,75-76H2,1-3H3,(H,77,83)(H,78,89)(H,97,98)(H,99,100)/b32-30+/t43?,44?,45-,46-,47?,48?,49-,50-,51-,53+,54+,55-,56?,57?,58+,59-,60-,61-,62-,63-,64+,65+,66+,67-,68+,69-,70+,73-,74+/m1/s1
InChI Key FFILOTSTFMXQJC-QCFYAKGBSA-N
Other ligands which bind to or alter the activity of this ligand
Key to terms and symbols Click column headers to sort
Ligand Sp. Type Action Value Parameter Concentration range (M) Reference
dinutuximab Peptide Approved drug Primary target of this compound Hs Antibody Binding 10.5 pKd - 2
⤷ pKd 10.5 (Kd 3x10-11 M) [2]
naxitamab Peptide Approved drug Primary target of this compound Hs Antibody Binding 8.5 pKd - 1
⤷ pKd 8.5 (Kd 3x10-9 M) [1]
Description: Affinity determined in a SPR assay, using whole antibody.