thymidine   Click here for help

GtoPdb Ligand ID: 4718

PDB Ligand
Compound class: Metabolite
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 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.

✖
Hydrogen bond acceptors 5
Hydrogen bond donors 3
Rotatable bonds 2
Topological polar surface area 104.55
Molecular weight 242.09
XLogP -0.59
No. Lipinski's rules broken 0

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
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.

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/)

✖
Canonical SMILES OCC1OC(CC1O)n1cc(C)c(=O)[nH]c1=O
Isomeric SMILES OC[C@H]1O[C@H](C[C@@H]1O)n1cc(C)c(=O)[nH]c1=O
InChI InChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1
InChI Key IQFYYKKMVGJFEH-XLPZGREQSA-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 Metabolite
IUPAC Name Click here for help
1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Database Links Click here for help
CAS Registry No. 50-89-5 (source: Scifinder)
ChEBI CHEBI:17748
ChEMBL Ligand CHEMBL52609
GtoPdb PubChem SID 178101429
PubChem CID 5789
RCSB PDB Ligand THM
Search Google for chemical match using the InChIKey IQFYYKKMVGJFEH-XLPZGREQSA-N
Search Google for chemicals with the same backbone IQFYYKKMVGJFEH
UniChem Compound Search for chemical match using the InChIKey IQFYYKKMVGJFEH-XLPZGREQSA-N
UniChem Connectivity Search for chemical match using the InChIKey IQFYYKKMVGJFEH-XLPZGREQSA-N
Wikipedia Thymidine