NPASS Compound

Natural Product: NPC491990

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 38 40 0 0 0 0 0 0 0 0999 V2000 -3.9915 -2.2785 -1.1290 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2402 -0.9776 -0.6145 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1483 -0.2238 -0.2379 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8376 -0.6770 -0.3394 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7672 0.0884 0.0407 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6172 -0.3378 -0.0451 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9338 -1.5793 -0.5310 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2871 -1.9467 -0.5948 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5944 -3.0671 -1.0320 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2278 -1.0467 -0.1682 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5557 -1.4025 -0.2288 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8845 -2.6580 -0.7197 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5409 -0.5386 0.1860 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1549 0.6983 0.6657 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1224 1.6036 1.0962 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8352 1.0572 0.7281 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8493 0.1986 0.3155 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5819 0.4787 0.3491 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0413 1.3578 0.5406 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3075 1.8474 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5066 3.1236 1.1672 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3760 1.0352 0.2608 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6318 1.5447 0.3886 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3456 2.2779 -0.5560 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9178 -2.7715 -1.4912 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2612 -2.1920 -1.9597 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5416 -2.8902 -0.2957 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6966 -1.6610 -0.7314 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1699 -2.2575 -0.8560 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3728 -3.2780 -0.0651 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5936 -0.7872 0.1516 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2379 2.4602 0.5486 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5583 2.0225 1.1040 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2075 1.9691 0.8428 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5411 3.2059 2.1747 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1257 1.6897 -1.0911 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7077 2.8495 -1.2626 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9248 3.0628 0.0110 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 1 0 6 7 2 0 7 8 1 0 8 9 2 0 8 10 1 0 10 11 2 0 11 12 1 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 5 19 2 0 19 20 1 0 20 21 1 0 20 22 2 0 22 23 1 0 23 24 1 0 22 3 1 0 18 6 1 0 17 10 1 0 1 25 1 0 1 26 1 0 1 27 1 0 4 28 1 0 7 29 1 0 12 30 1 0 13 31 1 0 15 32 1 0 16 33 1 0 19 34 1 0 21 35 1 0 24 36 1 0 24 37 1 0 24 38 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 NPC491990 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	30861
0.1-0.2	15840
0.2-0.3	2008
0.3-0.4	816
0.4-0.5	223
0.5-0.6	79
0.6-0.7	14
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	NPC606638
0.7925	Intermediate Similarity	NPC62536
0.7925	Intermediate Similarity	NPC601901
0.7818	Intermediate Similarity	NPC609179
0.75	Intermediate Similarity	NPC52005
0.75	Intermediate Similarity	NPC162351
0.75	Intermediate Similarity	NPC12200
0.7273	Intermediate Similarity	NPC120464
0.7273	Intermediate Similarity	NPC483773
0.7193	Intermediate Similarity	NPC177298
0.7069	Intermediate Similarity	NPC183950
0.6964	Remote Similarity	NPC231772
0.6842	Remote Similarity	NPC600900
0.6557	Remote Similarity	NPC605634
0.6379	Remote Similarity	NPC50403
0.6364	Remote Similarity	NPC175013
0.6308	Remote Similarity	NPC183
0.625	Remote Similarity	NPC279121
0.6207	Remote Similarity	NPC219330
0.6182	Remote Similarity	NPC50898
0.6182	Remote Similarity	NPC78540
0.6167	Remote Similarity	NPC54394
0.6102	Remote Similarity	NPC610359
0.6	Remote Similarity	NPC63454
0.6	Remote Similarity	NPC183851
0.5968	Remote Similarity	NPC133953
0.5932	Remote Similarity	NPC123886
0.5902	Remote Similarity	NPC159103
0.5833	Remote Similarity	NPC28274
0.5806	Remote Similarity	NPC603596
0.5738	Remote Similarity	NPC208197
0.5733	Remote Similarity	NPC101731
0.5714	Remote Similarity	NPC125062
0.5714	Remote Similarity	NPC481044
0.5667	Remote Similarity	NPC605617
0.5658	Remote Similarity	NPC165970
0.5658	Remote Similarity	NPC172202
0.5658	Remote Similarity	NPC284127
0.5645	Remote Similarity	NPC39732
0.5645	Remote Similarity	NPC82325
0.5645	Remote Similarity	NPC60972
0.5645	Remote Similarity	NPC29841
0.5645	Remote Similarity	NPC255350
0.5641	Remote Similarity	NPC84324
0.5584	Remote Similarity	NPC288131
0.5574	Remote Similarity	NPC33265
0.5574	Remote Similarity	NPC241838
0.557	Remote Similarity	NPC113163
0.5556	Remote Similarity	NPC272064
0.5556	Remote Similarity	NPC474520
0.5522	Remote Similarity	NPC112954
0.55	Remote Similarity	NPC66618
0.55	Remote Similarity	NPC305987
0.55	Remote Similarity	NPC75279
0.5493	Remote Similarity	NPC150908
0.5493	Remote Similarity	NPC600972
0.5484	Remote Similarity	NPC256283
0.5469	Remote Similarity	NPC279989
0.5455	Remote Similarity	NPC88023
0.5455	Remote Similarity	NPC309025
0.5432	Remote Similarity	NPC476410
0.5424	Remote Similarity	NPC274121
0.5417	Remote Similarity	NPC290830
0.5417	Remote Similarity	NPC71061
0.5417	Remote Similarity	NPC72425
0.5417	Remote Similarity	NPC303485
0.541	Remote Similarity	NPC241498
0.541	Remote Similarity	NPC284552
0.541	Remote Similarity	NPC184536
0.541	Remote Similarity	NPC103342
0.5342	Remote Similarity	NPC186227
0.5333	Remote Similarity	NPC213216
0.5323	Remote Similarity	NPC100887
0.5323	Remote Similarity	NPC286342
0.5323	Remote Similarity	NPC59951
0.5312	Remote Similarity	NPC160951
0.5312	Remote Similarity	NPC195202
0.5312	Remote Similarity	NPC223579
0.5312	Remote Similarity	NPC206604
0.527	Remote Similarity	NPC215203
0.5246	Remote Similarity	NPC293183
0.5246	Remote Similarity	NPC250822
0.5246	Remote Similarity	NPC610974
0.52	Remote Similarity	NPC601565
0.5195	Remote Similarity	NPC191306
0.5167	Remote Similarity	NPC179271
0.5161	Remote Similarity	NPC301323
0.5161	Remote Similarity	NPC156222
0.5156	Remote Similarity	NPC69394
0.5156	Remote Similarity	NPC83508
0.5143	Remote Similarity	NPC34089
0.5143	Remote Similarity	NPC196179
0.5139	Remote Similarity	NPC134796
0.5079	Remote Similarity	NPC48479
0.5079	Remote Similarity	NPC234133
0.5079	Remote Similarity	NPC120163
0.5079	Remote Similarity	NPC188203
0.5079	Remote Similarity	NPC276409
0.5077	Remote Similarity	NPC287101
0.5077	Remote Similarity	NPC235215
0.5077	Remote Similarity	NPC604422
0.5077	Remote Similarity	NPC607642
0.5072	Remote Similarity	NPC301217
0.507	Remote Similarity	NPC224714

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC491990 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6051
0.1-0.2	3038
0.2-0.3	52
0.3-0.4	6
0.4-0.5	0
0.5-0.6	1
0.6-0.7	1
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
0.625	Remote Similarity	NPD1511	Phase 2
0.5645	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