Natural Product: NPC609988

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

  Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
UNPD: Universal Natural Products Database [PMID: 23638153].
StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
MetaboLights: a metabolomics database [PMID: 27010336].
FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



  NP Quantity Composition/Concentration

Organism ID Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



 Biological Activity

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC609988 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.8936 High Similarity NPC607485
0.8881 High Similarity NPC610952
0.8431 Intermediate Similarity NPC477630
0.8333 Intermediate Similarity NPC601264
0.8182 Intermediate Similarity NPC600998
0.8182 Intermediate Similarity NPC611186
0.7727 Intermediate Similarity NPC477638
0.7687 Intermediate Similarity NPC610870
0.7584 Intermediate Similarity NPC603072
0.7568 Intermediate Similarity NPC604370
0.753 Intermediate Similarity NPC610704
0.745 Intermediate Similarity NPC477637
0.7436 Intermediate Similarity NPC477631
0.7178 Intermediate Similarity NPC610817
0.7143 Intermediate Similarity NPC607277
0.7105 Intermediate Similarity NPC600735
0.677 Remote Similarity NPC477639
0.6646 Remote Similarity NPC609634
0.6585 Remote Similarity NPC610535
0.645 Remote Similarity NPC605177
0.6412 Remote Similarity NPC611013
0.6407 Remote Similarity NPC600008
0.6407 Remote Similarity NPC603103
0.6407 Remote Similarity NPC604252
0.6358 Remote Similarity NPC603629
0.6358 Remote Similarity NPC606524
0.6265 Remote Similarity NPC611717
0.625 Remote Similarity NPC323927
0.6242 Remote Similarity NPC601051
0.6242 Remote Similarity NPC609990
0.6221 Remote Similarity NPC610649
0.6213 Remote Similarity NPC600634
0.6213 Remote Similarity NPC603201
0.619 Remote Similarity NPC607511
0.6095 Remote Similarity NPC477636
0.6065 Remote Similarity NPC604994
0.5897 Remote Similarity NPC611091
0.5848 Remote Similarity NPC608521
0.5818 Remote Similarity NPC606505
0.5799 Remote Similarity NPC601582
0.5799 Remote Similarity NPC603992
0.5799 Remote Similarity NPC610984
0.5796 Remote Similarity NPC604566
0.5747 Remote Similarity NPC600257
0.5689 Remote Similarity NPC478028
0.5663 Remote Similarity NPC478029
0.5629 Remote Similarity NPC610756
0.561 Remote Similarity NPC600192
0.5536 Remote Similarity NPC608676
0.5432 Remote Similarity NPC601205
0.539 Remote Similarity NPC473640
0.5381 Remote Similarity NPC607866
0.5354 Remote Similarity NPC605666
0.5337 Remote Similarity NPC604059
0.5305 Remote Similarity NPC603135
0.507 Remote Similarity NPC475506
0.5054 Remote Similarity NPC606286
0.5028 Remote Similarity NPC607892

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC609988 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
A: chemistry similarity;
B: biological targets similarity;
C: networks similarity;
D: cell-based bioactivity similarity;
E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data