NPASS Compound

Natural Product: NPC600241

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 64 69 0 0 0 0 0 0 0 0999 V2000 3.5691 3.3778 4.3753 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3463 3.3701 3.2157 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0786 2.6094 2.0861 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9975 1.7683 1.9933 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7809 1.0358 0.8450 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6259 1.1150 -0.2407 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3239 0.3001 -1.4306 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1132 0.3175 -2.5593 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8243 -0.4499 -3.6736 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5087 -0.4622 -4.7074 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6988 -1.2440 -3.6076 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3048 -2.0551 -4.6548 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0910 -2.0495 -5.8031 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1694 -2.8358 -4.5477 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4014 -2.8258 -3.3951 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7434 -3.5944 -3.2499 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7860 -2.0208 -2.3461 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0197 -1.9677 -1.1106 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0008 -1.0270 -1.0038 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7632 -0.9188 0.1268 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8508 0.0695 0.2700 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1829 0.9632 -0.7163 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2255 1.8802 -0.5255 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5394 2.7015 -1.4168 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9195 1.8795 0.6652 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9622 2.7694 0.9031 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2815 3.6681 -0.1135 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6540 2.7656 2.0953 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2631 1.8378 3.0398 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9438 1.8078 4.2584 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2292 0.9511 2.8114 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5307 0.9536 1.6103 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5473 0.1132 1.3878 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4926 -1.7838 1.1867 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4888 -2.7170 1.0959 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2737 -2.8141 -0.0548 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2973 -3.7348 -0.2020 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5599 -4.6140 0.8969 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9340 -1.2337 -2.4591 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2587 -0.4860 -1.4374 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7040 1.9555 -0.1448 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9384 2.7065 1.0145 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1338 3.9884 5.1364 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4469 2.3502 4.7789 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5514 3.8249 4.2269 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3127 1.6727 2.8103 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9175 0.3729 0.7889 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9895 0.9359 -2.6105 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1951 -2.9224 -6.3234 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8547 -3.4762 -5.3696 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9376 -3.9715 -2.3297 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1907 -0.3664 -1.8425 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6512 0.9741 -1.6464 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2177 4.6839 0.0214 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4577 3.4730 2.2411 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7400 1.2021 4.4282 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9242 0.2174 3.5654 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1025 -1.6822 2.0650 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2630 -3.4072 1.9244 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5288 -5.1573 0.7404 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6673 -4.0636 1.8471 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7279 -5.3478 0.9804 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3820 2.0341 -0.9860 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7901 3.3636 1.0762 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 12 14 1 0 14 15 2 0 15 16 1 0 15 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 23 25 1 0 25 26 2 0 26 27 1 0 26 28 1 0 28 29 2 0 29 30 1 0 29 31 1 0 31 32 2 0 32 33 1 0 20 34 2 0 34 35 1 0 35 36 2 0 36 37 1 0 37 38 1 0 17 39 2 0 39 40 1 0 6 41 1 0 41 42 2 0 42 3 1 0 40 7 1 0 39 11 1 0 36 18 1 0 33 21 1 0 32 25 1 0 1 43 1 0 1 44 1 0 1 45 1 0 4 46 1 0 5 47 1 0 8 48 1 0 13 49 1 0 14 50 1 0 16 51 1 0 19 52 1 0 22 53 1 0 27 54 1 0 28 55 1 0 30 56 1 0 31 57 1 0 34 58 1 0 35 59 1 0 38 60 1 0 38 61 1 0 38 62 1 0 41 63 1 0 42 64 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 NPC600241 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	30796
0.1-0.2	16362
0.2-0.3	1788
0.3-0.4	707
0.4-0.5	144
0.5-0.6	43
0.6-0.7	8
0.7-0.8	0
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC150908
0.8923	High Similarity	NPC71061
0.8235	Intermediate Similarity	NPC14606
0.8088	Intermediate Similarity	NPC303485
0.7971	Intermediate Similarity	NPC186227
0.7639	Intermediate Similarity	NPC265624
0.7541	Intermediate Similarity	NPC231772
0.7123	Intermediate Similarity	NPC215203
0.7083	Intermediate Similarity	NPC72425
0.7027	Intermediate Similarity	NPC601565
0.6667	Remote Similarity	NPC121649
0.6429	Remote Similarity	NPC138299
0.6351	Remote Similarity	NPC248739
0.6184	Remote Similarity	NPC290830
0.6176	Remote Similarity	NPC52005
0.6176	Remote Similarity	NPC12200
0.6154	Remote Similarity	NPC18699
0.6104	Remote Similarity	NPC194593
0.597	Remote Similarity	NPC483773
0.5949	Remote Similarity	NPC205026
0.5897	Remote Similarity	NPC159707
0.5735	Remote Similarity	NPC241838
0.5735	Remote Similarity	NPC62536
0.5735	Remote Similarity	NPC120464
0.5735	Remote Similarity	NPC601901
0.5733	Remote Similarity	NPC183
0.5733	Remote Similarity	NPC254351
0.5732	Remote Similarity	NPC55443
0.5658	Remote Similarity	NPC610480
0.5641	Remote Similarity	NPC600972
0.5634	Remote Similarity	NPC183950
0.5588	Remote Similarity	NPC52611
0.5588	Remote Similarity	NPC156222
0.5588	Remote Similarity	NPC29353
0.5584	Remote Similarity	NPC259757
0.557	Remote Similarity	NPC158027
0.5556	Remote Similarity	NPC67322
0.5538	Remote Similarity	NPC50898
0.5538	Remote Similarity	NPC78540
0.5507	Remote Similarity	NPC184136
0.5507	Remote Similarity	NPC59951
0.5493	Remote Similarity	NPC606638
0.5479	Remote Similarity	NPC605634
0.5467	Remote Similarity	NPC288840
0.5455	Remote Similarity	NPC222713
0.5432	Remote Similarity	NPC143851
0.5429	Remote Similarity	NPC603662
0.5417	Remote Similarity	NPC610914
0.5362	Remote Similarity	NPC600177
0.5333	Remote Similarity	NPC111112
0.5309	Remote Similarity	NPC272064
0.5286	Remote Similarity	NPC266597
0.5211	Remote Similarity	NPC600900
0.5147	Remote Similarity	NPC279121
0.5128	Remote Similarity	NPC196179
0.507	Remote Similarity	NPC57030
0.507	Remote Similarity	NPC145379
0.5065	Remote Similarity	NPC112954
0.5063	Remote Similarity	NPC280975
0.5062	Remote Similarity	NPC601984
0.5062	Remote Similarity	NPC603508

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC600241 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5898
0.1-0.2	3189
0.2-0.3	53
0.3-0.4	7
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	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.5147	Remote Similarity	NPD1511	Phase 2

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