NPASS Compound

Natural Product: NPC600539

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

Chemical Representations

RDKit 3D 26 28 0 0 0 0 0 0 0 0999 V2000 -0.6334 2.6317 0.1869 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3204 1.4152 0.1179 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0677 0.9913 0.1631 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1050 1.8913 0.2828 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4285 1.5285 0.3287 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7329 0.1855 0.2504 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7504 -0.7534 0.1309 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0226 -2.1274 0.0486 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4286 -0.3474 0.0881 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3918 -1.3710 -0.0403 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6699 -2.6073 -0.1125 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9965 -0.9283 -0.0841 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9994 -1.8970 -0.2068 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3192 -1.4967 -0.2499 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6955 -0.1675 -0.1764 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6966 0.7760 -0.0557 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0144 2.1247 0.0223 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3680 0.4015 -0.0103 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8778 2.9442 0.3448 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2380 2.2445 0.4231 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7576 -0.1689 0.2808 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0805 -2.5303 -0.8983 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7103 -2.9463 -0.2653 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1157 -2.2418 -0.3456 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7520 0.0885 -0.2155 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9299 2.3605 0.3989 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 7 9 2 0 9 10 1 0 10 11 2 0 10 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 1 0 16 18 2 0 18 2 1 0 9 3 1 0 18 12 1 0 4 19 1 0 5 20 1 0 6 21 1 0 8 22 1 0 13 23 1 0 14 24 1 0 15 25 1 0 17 26 1 0 M END

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

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 NPC600539 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	23761
0.1-0.2	22128
0.2-0.3	3505
0.3-0.4	330
0.4-0.5	82
0.5-0.6	36
0.6-0.7	7
0.7-0.8	0
0.8-0.85	0
0.85-0.9	3
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC375356
0.8846	High Similarity	NPC300274
0.8846	High Similarity	NPC608834
0.88	High Similarity	NPC103540
0.7097	Intermediate Similarity	NPC604340
0.7037	Intermediate Similarity	NPC96915
0.6765	Remote Similarity	NPC199253
0.6765	Remote Similarity	NPC205992
0.6667	Remote Similarity	NPC99731
0.6471	Remote Similarity	NPC282923
0.6286	Remote Similarity	NPC416
0.6111	Remote Similarity	NPC70622
0.6053	Remote Similarity	NPC21599
0.5946	Remote Similarity	NPC487321
0.5938	Remote Similarity	NPC142956
0.5789	Remote Similarity	NPC257644
0.5758	Remote Similarity	NPC294226
0.575	Remote Similarity	NPC474813
0.5641	Remote Similarity	NPC288089
0.5641	Remote Similarity	NPC604901
0.5641	Remote Similarity	NPC608971
0.561	Remote Similarity	NPC255641
0.561	Remote Similarity	NPC37220
0.5588	Remote Similarity	NPC31799
0.55	Remote Similarity	NPC124365
0.5476	Remote Similarity	NPC242994
0.5476	Remote Similarity	NPC605722
0.5455	Remote Similarity	NPC147418
0.5366	Remote Similarity	NPC1268
0.5366	Remote Similarity	NPC302783
0.5349	Remote Similarity	NPC169452
0.5349	Remote Similarity	NPC193555
0.5349	Remote Similarity	NPC245923
0.5349	Remote Similarity	NPC272268
0.5294	Remote Similarity	NPC44437
0.5238	Remote Similarity	NPC66593
0.5238	Remote Similarity	NPC606400
0.5227	Remote Similarity	NPC225051
0.5227	Remote Similarity	NPC205982
0.5172	Remote Similarity	NPC224584
0.5143	Remote Similarity	NPC608942
0.5135	Remote Similarity	NPC607416
0.5122	Remote Similarity	NPC252208
0.5122	Remote Similarity	NPC226578
0.5116	Remote Similarity	NPC610494
0.5111	Remote Similarity	NPC61531
0.5111	Remote Similarity	NPC79627
0.5111	Remote Similarity	NPC181560
0.5111	Remote Similarity	NPC80035

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC600539 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3707
0.1-0.2	5047
0.2-0.3	374
0.3-0.4	18
0.4-0.5	2
0.5-0.6	1
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.88	High Similarity	NPD1470	Phase 4
0.5806	Remote Similarity	NPD1201	Phase 4

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