cyclic di-GMP   Click here for help

GtoPdb Ligand ID: 13137

Synonyms: Bis-(3'-5')-cyclic dimeric guanosine monophosphate | c-di-GMP | cGpGp | dyclic diguanylate monophosphate
PDB Ligand Immunopharmacology Ligand
Compound class: Synthetic organic
Comment: Cyclic di-GMP is a dinucleotide of bacterial origin that acts as a signalling molecule in prokaryotes. In mammals it acts as a STING (stimulator of IFN genes) agonist that promotes the type I interferon inflammatory response [1-2].
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 24
Hydrogen bond donors 8
Rotatable bonds 2
Topological polar surface area 356.22
Molecular weight 690.41
XLogP -6.68
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 C1[C@@H]2[C@H]([C@H]([C@H](N3C=NC4=C3N=C(N)NC4=O)O2)O)OP(=O)(O)OC[C@@H]5[C@H]([C@H]([C@H](N6C=NC7=C6N=C(N)NC7=O)O5)O)OP(=O)(O)O1
Isomeric SMILES C1[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=NC4=C3N=C(NC4=O)N)O)OP(=O)(OC[C@@H]5[C@H]([C@H]([C@@H](O5)N6C=NC7=C6N=C(NC7=O)N)O)OP(=O)(O1)O)O
InChI InChI=1S/C20H24N10O14P2/c21-19-25-13-7(15(33)27-19)23-3-29(13)17-9(31)11-5(41-17)1-39-45(35,36)44-12-6(2-40-46(37,38)43-11)42-18(10(12)32)30-4-24-8-14(30)26-20(22)28-16(8)34/h3-6,9-12,17-18,31-32H,1-2H2,(H,35,36)(H,37,38)(H3,21,25,27,33)(H3,22,26,28,34)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1
InChI Key PKFDLKSEZWEFGL-MHARETSRSA-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/)
Classification Click here for help
Compound class Synthetic organic
Synonyms Click here for help
Bis-(3'-5')-cyclic dimeric guanosine monophosphate | c-di-GMP | cGpGp | dyclic diguanylate monophosphate
Database Links Click here for help
BindingDB Ligand 50436163
ChEBI CHEBI:49537
ChEMBL Ligand CHEMBL1231573
GtoPdb PubChem SID 491299919
PubChem CID 135440063
RCSB PDB Ligand C2E
Search Google for chemical match using the InChIKey PKFDLKSEZWEFGL-MHARETSRSA-N
Search Google for chemicals with the same backbone PKFDLKSEZWEFGL
UniChem Compound Search for chemical match using the InChIKey PKFDLKSEZWEFGL-MHARETSRSA-N
UniChem Connectivity Search for chemical match using the InChIKey PKFDLKSEZWEFGL-MHARETSRSA-N