Help - How to use PungenDB

Compounds search Simple

To Search PungentDB Compounds enter your query in the search box and click search. You can enter compound name, PubChem CID, SMILES, CAS number, Formula, FEMA number, InChI, InChI Key, CAS registry number, IUPAC systematic name and properties. For search by specific criteria please go to advanced search.

PungentDB Advanced Search

This search form contains a number of fields, all of which are optional (although at least one field is needed to perform a search).

Structure Similarity Search

Search PungentDB compounds by Similarity 2D Structure Similarity Search allows to locate records that are similar to a chemical structure query. You can draw a molecule in the upper box. Similarity is measured by the Tanimoto equation and the fingerprint. This fingerprint consists of series of chemical substructure "keys". Each key denotes the presence or absence of a particular substructure in a molecule. The fingerprint does not consider variation in stereochemical or isotopic information. Collectively, these binary keys provide a "fingerprint" of a particular chemical structure valence-bond form. We used rdkit [1] for calculating smiles fingerprints and for the similarity search.

References

[1] http://www.rdkit.org

[2] Landrum G. RDKit: Open-source cheminformatics[J]. 2006.

[3] Landrum G. RDKit: open-source cheminformatics http://www.rdkit. org[J]. 2016.

Known Targets: Note: Known Targets (Gene) from 6952 literatures, DrugBank (http://www.drugbank.ca/), STITCH (http://stitch.embl.de/), ChEMBL (https://www.ebi.ac.uk/chembl/), Therapeutic Target Database (http://bidd.nus.edu.sg/group/ttd/), and Comparative Toxicogenomics Database (CTD, http://ctdbase.org/). This section also holds information on the Pungent Taste Associated Receptors and Olfactory Receptors taste receptors (human, rat, mouse, etc) that bind this compound, if known from the literature. A link to the publication which showed this ligand-receptor interaction is given in the reference column. In specific organism mode only targets off the selected organism would be shown

Assay: This section holds quantitative EC50 or IC50 data that was collected from publications in which assay tests to detect pungent compounds were effected pungent taste associated receptors and olfactory receptors.

Compound Properties

The following physical properties were computed by RDKit (Open-source cheminformatics; http://www.rdkit.org) for each compound

• Molecular Weight (g/mol)
• AlogP: Log of the octanol-water partition coefficient using using Crippen's approach.[1]
• Hydrogen Bond Acceptors: Hydrogen bond acceptors are defined as heteroatoms (Oxygen, Nitrogen, Sulfur or Phosphorus) with one or more lone electron pairs, excluding atoms with positive formal charges, amide and pyrrole-type Nitrogens, and aromatic Oxygen and Sulfur atoms in heterocyclic rings
• Hydrogen Bond Donors: Hydrogen Bond Donors are defined as heteroatoms (Oxygen, Nitrogen, Sulfur, or Phosphorus) with one or more attached Hydrogen atoms.
• Rotatable Bonds: Rotatable bonds, defined as single bonds between heavy atoms that are both not in a ring and not terminal, i.e., connected to a heavy atom that is attached to only hydrogens. As a special case, amide C-N bonds are not rotatable.

For each compound three identifiers are displayed: IUPAC systematic name, CAS registry number [2] and Smiles. (The first two fields are not always present)

IUPAC Systematic name

Standard IUPAC systematic name for compound. Was taken from PubChem

CAS Registry Number

are unique numerical identifiers assigned by the "Chemical Abstracts Service" to every chemical described in the open scientific literature (currently including those described from at least 1957 through the present) [2]

SMILES

Simplified Molecular Input Line Entry Specification is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings

Compound Display The compound display is powered by MarvinView (ChemAxon). Double clicking on the image will open a MarvinView applet window, providing various molecule rendering and viewing options. A combination of clicking on the image and mouse moving will rotate the compound. For further help regarding the MarvinView applet, use the help section in the MarvinView applet windows.

Compound Download The download button enables the user to download the compound 2D structure in different formats: SDF file, Smiles file or Image file.

References

[1] S. A. Wildman and G. M. Crippen *JCICS* _39_ 868-873 (1999)

[2] CAS registry description , by the Chemical Abstracts Service

References Several properties are displayed for each bitter taste receptor

Organism

the link to the 3D structure of this receptor.

Number of known pungent ligands of the receptor, according to the data collected by us.

function of each receptor

Protein sequence (six format files, eg, FASTA sequence, PDB format, PDB fomat(gz), PDBx/mmCIF Format, PDBx/mmCIF Format (gz), PDBML/XML Format (gz))

Function

Known Ligands For each Pungent Taste Associated Receptors and Olfactory Receptors in the database, a list of its known Pungent Taste Associated Receptors and Olfactory Receptors’ligands, as collected from the literature, is displayed. Clicking the ligand name opens the PungentDB compound entry. The user can download the ligand structures as a 2D (3D) SDF and xml format file by checking the ligand checkboxes and clicking the Download SDF or xml button.

3D Homology Mode This is a 3D visualization of a homology model created for this receptor, shown in ribbon view. Downloading the PDB file of the model is possible via the download link on the right side of the visualizer.

Protein diagram The 3D protein diagram is based on protein secondary structure prediction performed using

References

[1] Hennerdal A, Elofsson A (2011) Rapid membrane protein topology prediction. Bioinformatics. 27(9):1322-3 PubMedID: 21493661

[2] Ballesteros J, Weinstein H (1995) Integrated methods for the construction of three- dimensional models of structure-function relations in G protein-coupled receptors. Methods Neurosci 25:366-428.

Properties

[1] Liang F, Li L, Wang M, et al. Molecular network and chemical fragment-based characteristics of medicinal herbs with cold and hot properties from Chinese medicine[J]. Journal of ethnopharmacology, 2013, 148(3): 770-779.

[2] Zhang T. Chinese materia medica. Beijing: High Education Press; 2008.

[3] Ung C Y, Li H, Kong C Y, et al. Usefulness of traditionally defined herbal properties for distinguishing prescriptions of traditional Chinese medicine from non-prescription recipes[J]. Journal of ethnopharmacology, 2007, 109(1): 21-28.

[4] Yanling Z, Yun W, Yanjiang Q. Research on material base of TCM property based on pharmacophore[J]. World Science and Technology, 2009, 11(5): 735-738.

[5] Zhou J, Xie G, Yan X. Encyclopedia of traditional Chinese medicines[J]. Isolat Compound AB, 2011, 1: 455.

[6] Chen Z, Cao Y, He S, et al. Development of models for classification of action between heat-clearing herbs and blood-activating stasis-resolving herbs based on theory of traditional Chinese medicine[J]. Chinese medicine, 2018, 13(1): 12.