Natural Product: NPC604573

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 NPC604573 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
1.0 High Similarity NPC95145
1.0 High Similarity NPC325642
1.0 High Similarity NPC65174
0.8929 High Similarity NPC424
0.8929 High Similarity NPC36061
0.8929 High Similarity NPC69510
0.8929 High Similarity NPC77272
0.8929 High Similarity NPC290563
0.8929 High Similarity NPC139029
0.8929 High Similarity NPC281972
0.8929 High Similarity NPC261831
0.8929 High Similarity NPC87564
0.8571 High Similarity NPC281245
0.8276 Intermediate Similarity NPC92114
0.8065 Intermediate Similarity NPC154245
0.8065 Intermediate Similarity NPC85813
0.8065 Intermediate Similarity NPC223697
0.8065 Intermediate Similarity NPC6095
0.7742 Intermediate Similarity NPC321062
0.7407 Intermediate Similarity NPC171736
0.7407 Intermediate Similarity NPC301585
0.7407 Intermediate Similarity NPC261080
0.7407 Intermediate Similarity NPC132565
0.7407 Intermediate Similarity NPC209970
0.7407 Intermediate Similarity NPC216630
0.7407 Intermediate Similarity NPC201844
0.7407 Intermediate Similarity NPC301696
0.7407 Intermediate Similarity NPC196924
0.7407 Intermediate Similarity NPC307783
0.7407 Intermediate Similarity NPC154186
0.7407 Intermediate Similarity NPC149184
0.7407 Intermediate Similarity NPC279026
0.7407 Intermediate Similarity NPC113928
0.7407 Intermediate Similarity NPC14227
0.7297 Intermediate Similarity NPC251042
0.7297 Intermediate Similarity NPC255863
0.7297 Intermediate Similarity NPC174447
0.7297 Intermediate Similarity NPC136164
0.7297 Intermediate Similarity NPC122521
0.7297 Intermediate Similarity NPC245947
0.7188 Intermediate Similarity NPC5413
0.7105 Intermediate Similarity NPC318420
0.7105 Intermediate Similarity NPC326268
0.7037 Intermediate Similarity NPC155263
0.697 Remote Similarity NPC52955
0.697 Remote Similarity NPC88966
0.697 Remote Similarity NPC25417
0.697 Remote Similarity NPC1813
0.697 Remote Similarity NPC59051
0.6757 Remote Similarity NPC106851
0.6757 Remote Similarity NPC282788
0.6757 Remote Similarity NPC274927
0.6757 Remote Similarity NPC477201
0.6667 Remote Similarity NPC180534
0.6667 Remote Similarity NPC91495
0.6667 Remote Similarity NPC70387
0.6667 Remote Similarity NPC611531
0.6579 Remote Similarity NPC179764
0.641 Remote Similarity NPC243532
0.6296 Remote Similarity NPC214610
0.6296 Remote Similarity NPC118968
0.6296 Remote Similarity NPC183424
0.6296 Remote Similarity NPC294085
0.625 Remote Similarity NPC68343
0.625 Remote Similarity NPC34416
0.625 Remote Similarity NPC328089
0.6216 Remote Similarity NPC487561
0.6216 Remote Similarity NPC225929
0.6216 Remote Similarity NPC606120
0.6071 Remote Similarity NPC175342
0.6061 Remote Similarity NPC8219
0.6 Remote Similarity NPC473863
0.5926 Remote Similarity NPC268826
0.5882 Remote Similarity NPC18712
0.5882 Remote Similarity NPC149821
0.5882 Remote Similarity NPC74845
0.5714 Remote Similarity NPC320642
0.5714 Remote Similarity NPC87394
0.5714 Remote Similarity NPC324004
0.5714 Remote Similarity NPC328497
0.5714 Remote Similarity NPC329550
0.5714 Remote Similarity NPC602547
0.5676 Remote Similarity NPC40082
0.5625 Remote Similarity NPC55023
0.5625 Remote Similarity NPC21844
0.561 Remote Similarity NPC187777
0.561 Remote Similarity NPC318814
0.561 Remote Similarity NPC320669
0.5588 Remote Similarity NPC129972
0.5588 Remote Similarity NPC301528
0.5588 Remote Similarity NPC71317
0.5588 Remote Similarity NPC163746
0.5588 Remote Similarity NPC103286
0.5588 Remote Similarity NPC184171
0.5581 Remote Similarity NPC323045
0.5581 Remote Similarity NPC317881
0.5556 Remote Similarity NPC174368
0.5556 Remote Similarity NPC174560
0.5556 Remote Similarity NPC125312
0.5484 Remote Similarity NPC604140
0.5455 Remote Similarity NPC322461
0.5429 Remote Similarity NPC207292
0.5366 Remote Similarity NPC274290
0.5357 Remote Similarity NPC134782
0.5333 Remote Similarity NPC605544
0.5333 Remote Similarity NPC607260
0.5294 Remote Similarity NPC314679
0.5294 Remote Similarity NPC262968
0.5278 Remote Similarity NPC48162
0.5238 Remote Similarity NPC323597
0.5238 Remote Similarity NPC211752
0.5238 Remote Similarity NPC323498
0.5238 Remote Similarity NPC99619
0.5227 Remote Similarity NPC49863
0.5217 Remote Similarity NPC329249
0.5217 Remote Similarity NPC92558
0.5122 Remote Similarity NPC28205
0.5116 Remote Similarity NPC317583

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC604573 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
0.8929 High Similarity NPD3195 Phase 2
0.8929 High Similarity NPD3196 Approved
0.8065 Intermediate Similarity NPD4266 Phase 2
0.7407 Intermediate Similarity NPD2270 Pre-clinical
0.7407 Intermediate Similarity NPD633 Phase 3
0.7407 Intermediate Similarity NPD9448 Phase 2
0.7188 Intermediate Similarity NPD3173 Phase 4
0.7143 Intermediate Similarity NPD3194 Phase 4
0.697 Remote Similarity NPD3172 Approved
0.6667 Remote Similarity NPD622 Pre-clinical
0.6296 Remote Similarity NPD9655 Phase 4
0.625 Remote Similarity NPD39 Phase 4
0.5714 Remote Similarity NPD3199 Clinical (unspecified phase)
0.5294 Remote Similarity NPD28 Approved
0.5294 Remote Similarity NPD29 Phase 4
0.5227 Remote Similarity NPD4247 Clinical (unspecified phase)

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