NPASS Compound

Natural Product: NPC590995

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 41 43 0 0 0 0 0 0 0 0999 V2000 5.4635 2.0903 1.1688 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9755 0.9030 0.6159 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6269 0.7058 0.4600 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7047 1.6643 0.8397 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3614 1.3959 0.6529 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9013 0.2099 0.1027 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5130 0.0648 -0.0777 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1470 -1.1015 -0.3982 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5023 -2.3158 -0.5850 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3554 -3.2177 0.5136 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5430 -1.1598 -0.5594 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1331 -2.2201 -0.8544 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2957 -0.0186 -0.3894 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6672 -0.0243 -0.5356 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3197 -1.2025 -0.8632 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3613 1.1544 -0.3501 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6661 2.2930 -0.0267 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3361 3.5118 0.1701 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2990 2.2807 0.1150 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5888 1.1230 -0.0642 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3116 1.1175 0.0693 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8194 -0.7295 -0.2700 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1912 -0.4778 -0.0886 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1194 -1.4274 -0.4642 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6731 -2.6430 -1.0275 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2953 2.9617 0.4880 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9126 2.3265 2.1048 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5345 2.0365 1.4491 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0619 2.5859 1.2680 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6436 2.1459 0.9507 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0771 -4.0447 0.4617 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4577 -2.6250 1.4397 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6589 -3.6416 0.4766 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6223 -1.7877 -0.0815 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4363 1.2010 -0.4535 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9764 4.3393 -0.2958 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7413 3.1851 0.3724 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5860 -1.6672 -0.7256 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6091 -3.2052 -1.3152 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0229 -2.5004 -1.9123 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1894 -3.2862 -0.2502 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 1 0 8 11 1 0 11 12 2 0 11 13 1 0 13 14 2 0 14 15 1 0 14 16 1 0 16 17 2 0 17 18 1 0 17 19 1 0 19 20 2 0 20 21 1 0 6 22 1 0 22 23 2 0 23 24 1 0 24 25 1 0 23 3 1 0 21 7 1 0 20 13 1 0 1 26 1 0 1 27 1 0 1 28 1 0 4 29 1 0 5 30 1 0 10 31 1 0 10 32 1 0 10 33 1 0 15 34 1 0 16 35 1 0 18 36 1 0 19 37 1 0 22 38 1 0 25 39 1 0 25 40 1 0 25 41 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 NPC590995 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	28372
0.1-0.2	18184
0.2-0.3	2173
0.3-0.4	635
0.4-0.5	365
0.5-0.6	95
0.6-0.7	9
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC603596
0.7925	Intermediate Similarity	NPC59951
0.7925	Intermediate Similarity	NPC610359
0.7636	Intermediate Similarity	NPC82325
0.75	Intermediate Similarity	NPC162351
0.7407	Intermediate Similarity	NPC184536
0.7407	Intermediate Similarity	NPC103342
0.7368	Intermediate Similarity	NPC279989
0.7321	Intermediate Similarity	NPC115798
0.7321	Intermediate Similarity	NPC159103
0.7273	Intermediate Similarity	NPC286342
0.7193	Intermediate Similarity	NPC236769
0.7193	Intermediate Similarity	NPC12200
0.7091	Intermediate Similarity	NPC123886
0.6724	Remote Similarity	NPC176300
0.6441	Remote Similarity	NPC178854
0.6333	Remote Similarity	NPC7846
0.6333	Remote Similarity	NPC605494
0.619	Remote Similarity	NPC158874
0.6167	Remote Similarity	NPC54394
0.6102	Remote Similarity	NPC241838
0.6094	Remote Similarity	NPC99671
0.6034	Remote Similarity	NPC259058
0.5932	Remote Similarity	NPC219330
0.5882	Remote Similarity	NPC470458
0.5882	Remote Similarity	NPC269285
0.5846	Remote Similarity	NPC269906
0.5833	Remote Similarity	NPC231772
0.5833	Remote Similarity	NPC62536
0.5821	Remote Similarity	NPC97255
0.5806	Remote Similarity	NPC52005
0.5806	Remote Similarity	NPC200316
0.5806	Remote Similarity	NPC606638
0.5806	Remote Similarity	NPC609179
0.5781	Remote Similarity	NPC605634
0.5763	Remote Similarity	NPC472438
0.5738	Remote Similarity	NPC9609
0.5692	Remote Similarity	NPC76482
0.5667	Remote Similarity	NPC203891
0.5667	Remote Similarity	NPC299923
0.5667	Remote Similarity	NPC262094
0.5667	Remote Similarity	NPC310259
0.5645	Remote Similarity	NPC29841
0.5588	Remote Similarity	NPC259632
0.5588	Remote Similarity	NPC183
0.5574	Remote Similarity	NPC50403
0.5574	Remote Similarity	NPC28274
0.5574	Remote Similarity	NPC76376
0.5526	Remote Similarity	NPC609478
0.5507	Remote Similarity	NPC56786
0.5479	Remote Similarity	NPC470461
0.5469	Remote Similarity	NPC133953
0.5469	Remote Similarity	NPC125062
0.5467	Remote Similarity	NPC472459
0.5455	Remote Similarity	NPC603082
0.541	Remote Similarity	NPC266960
0.5397	Remote Similarity	NPC50728
0.5397	Remote Similarity	NPC270620
0.5397	Remote Similarity	NPC166753
0.5397	Remote Similarity	NPC255350
0.5395	Remote Similarity	NPC219904
0.5393	Remote Similarity	NPC477895
0.5352	Remote Similarity	NPC280493
0.5333	Remote Similarity	NPC201547
0.5325	Remote Similarity	NPC120099
0.5323	Remote Similarity	NPC214138
0.5323	Remote Similarity	NPC110070
0.5323	Remote Similarity	NPC146679
0.5323	Remote Similarity	NPC120464
0.5323	Remote Similarity	NPC163524
0.5323	Remote Similarity	NPC483773
0.5323	Remote Similarity	NPC601901
0.5312	Remote Similarity	NPC25495
0.5312	Remote Similarity	NPC206604
0.5312	Remote Similarity	NPC604422
0.5256	Remote Similarity	NPC223747
0.5246	Remote Similarity	NPC607530
0.5238	Remote Similarity	NPC600900
0.5231	Remote Similarity	NPC183950
0.5231	Remote Similarity	NPC34725
0.5231	Remote Similarity	NPC78326
0.5222	Remote Similarity	NPC48984
0.52	Remote Similarity	NPC470460
0.52	Remote Similarity	NPC64305
0.5195	Remote Similarity	NPC175107
0.519	Remote Similarity	NPC203050
0.519	Remote Similarity	NPC225434
0.5167	Remote Similarity	NPC179271
0.5161	Remote Similarity	NPC287979
0.5161	Remote Similarity	NPC103904
0.5156	Remote Similarity	NPC300943
0.5156	Remote Similarity	NPC253634
0.5152	Remote Similarity	NPC483775
0.5147	Remote Similarity	NPC153512
0.5139	Remote Similarity	NPC54802
0.5139	Remote Similarity	NPC197304
0.5079	Remote Similarity	NPC149127
0.5079	Remote Similarity	NPC32557
0.5079	Remote Similarity	NPC260895
0.5079	Remote Similarity	NPC176665
0.5079	Remote Similarity	NPC188871
0.5079	Remote Similarity	NPC101830
0.5077	Remote Similarity	NPC224137
0.5077	Remote Similarity	NPC104459
0.5077	Remote Similarity	NPC195202
0.5077	Remote Similarity	NPC236223
0.5077	Remote Similarity	NPC603112
0.5068	Remote Similarity	NPC288084
0.5068	Remote Similarity	NPC276222
0.5068	Remote Similarity	NPC274618
0.5068	Remote Similarity	NPC118284
0.5068	Remote Similarity	NPC608147
0.5067	Remote Similarity	NPC104677
0.5065	Remote Similarity	NPC216496
0.5065	Remote Similarity	NPC325555
0.5065	Remote Similarity	NPC226304
0.5063	Remote Similarity	NPC88023
0.5063	Remote Similarity	NPC309025

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC590995 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5289
0.1-0.2	3780
0.2-0.3	70
0.3-0.4	6
0.4-0.5	3
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
0.5397	Remote Similarity	NPD2801	Pre-clinical

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