NPASS Compound

Natural Product: NPC606283

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 34 36 0 0 0 0 0 0 0 0999 V2000 -3.5444 1.8208 2.1889 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1780 0.8372 1.4348 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5193 -0.0278 0.5643 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1538 0.0485 0.3985 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4439 -0.7925 -0.4596 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0037 -0.6663 -0.5959 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7616 -1.4575 -1.4184 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1455 -1.3174 -1.5316 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8301 -2.0414 -2.2828 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7336 -0.3326 -0.7687 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1155 -0.1161 -0.8147 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8333 -0.9465 -1.6648 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7066 0.8693 -0.0519 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9197 1.6509 0.7673 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4933 2.6627 1.5562 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5592 1.4335 0.8088 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9343 0.4425 0.0468 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6373 0.2565 0.1049 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1851 -1.7205 -1.1466 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5759 -1.8040 -0.9827 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2568 -0.9638 -0.1303 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6372 -1.0367 0.0411 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4253 2.7384 1.5724 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6003 1.4208 2.5787 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2271 2.0664 3.0511 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5652 0.7769 0.9366 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2955 -2.2184 -2.0058 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5571 -0.6321 -2.2884 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7801 1.0193 -0.1034 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1055 2.3400 2.3181 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9689 2.0521 1.4515 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6835 -2.4058 -1.8327 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1069 -2.5481 -1.5444 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2780 -1.4085 -0.6200 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 2 0 21 22 1 0 21 3 1 0 18 6 1 0 17 10 1 0 1 23 1 0 1 24 1 0 1 25 1 0 4 26 1 0 7 27 1 0 12 28 1 0 13 29 1 0 15 30 1 0 16 31 1 0 19 32 1 0 20 33 1 0 22 34 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 NPC606283 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	30383
0.1-0.2	15835
0.2-0.3	2371
0.3-0.4	854
0.4-0.5	263
0.5-0.6	99
0.6-0.7	26
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	NPC183950
0.7778	Intermediate Similarity	NPC120464
0.75	Intermediate Similarity	NPC83508
0.7368	Intermediate Similarity	NPC52005
0.7368	Intermediate Similarity	NPC12200
0.7241	Intermediate Similarity	NPC125062
0.7241	Intermediate Similarity	NPC279989
0.7241	Intermediate Similarity	NPC137062
0.7143	Intermediate Similarity	NPC231772
0.7143	Intermediate Similarity	NPC62536
0.7143	Intermediate Similarity	NPC483773
0.7143	Intermediate Similarity	NPC601901
0.7069	Intermediate Similarity	NPC115323
0.7069	Intermediate Similarity	NPC606638
0.6981	Remote Similarity	NPC50898
0.6727	Remote Similarity	NPC279121
0.6724	Remote Similarity	NPC312924
0.6667	Remote Similarity	NPC112954
0.6667	Remote Similarity	NPC47781
0.6528	Remote Similarity	NPC601710
0.6486	Remote Similarity	NPC4390
0.6462	Remote Similarity	NPC183
0.6452	Remote Similarity	NPC605634
0.6441	Remote Similarity	NPC600900
0.6393	Remote Similarity	NPC227325
0.6364	Remote Similarity	NPC78540
0.6333	Remote Similarity	NPC280339
0.6333	Remote Similarity	NPC20830
0.6324	Remote Similarity	NPC600972
0.6269	Remote Similarity	NPC602497
0.6232	Remote Similarity	NPC290830
0.6232	Remote Similarity	NPC303485
0.623	Remote Similarity	NPC4455
0.623	Remote Similarity	NPC128863
0.614	Remote Similarity	NPC274121
0.6129	Remote Similarity	NPC606105
0.6102	Remote Similarity	NPC241498
0.6034	Remote Similarity	NPC213216
0.6	Remote Similarity	NPC71061
0.6	Remote Similarity	NPC72425
0.5972	Remote Similarity	NPC601565
0.5965	Remote Similarity	NPC175013
0.5932	Remote Similarity	NPC610974
0.5915	Remote Similarity	NPC272064
0.5897	Remote Similarity	NPC113163
0.5833	Remote Similarity	NPC301323
0.5833	Remote Similarity	NPC284552
0.5833	Remote Similarity	NPC215203
0.5833	Remote Similarity	NPC103342
0.5823	Remote Similarity	NPC66618
0.5823	Remote Similarity	NPC305987
0.5806	Remote Similarity	NPC167815
0.5789	Remote Similarity	NPC172202
0.5789	Remote Similarity	NPC284127
0.5758	Remote Similarity	NPC138299
0.5758	Remote Similarity	NPC111112
0.5738	Remote Similarity	NPC100887
0.5738	Remote Similarity	NPC286342
0.5738	Remote Similarity	NPC234133
0.5738	Remote Similarity	NPC28274
0.5735	Remote Similarity	NPC34089
0.5735	Remote Similarity	NPC196179
0.5714	Remote Similarity	NPC610401
0.5694	Remote Similarity	NPC63454
0.5694	Remote Similarity	NPC183851
0.5672	Remote Similarity	NPC301217
0.5672	Remote Similarity	NPC291746
0.5634	Remote Similarity	NPC150908
0.5625	Remote Similarity	NPC133953
0.56	Remote Similarity	NPC475942
0.5584	Remote Similarity	NPC165970
0.557	Remote Similarity	NPC84324
0.5556	Remote Similarity	NPC82325
0.5556	Remote Similarity	NPC54394
0.5556	Remote Similarity	NPC253634
0.5556	Remote Similarity	NPC255350
0.5538	Remote Similarity	NPC254702
0.5513	Remote Similarity	NPC288131
0.5484	Remote Similarity	NPC48479
0.5484	Remote Similarity	NPC198826
0.5484	Remote Similarity	NPC188203
0.5479	Remote Similarity	NPC186227
0.5469	Remote Similarity	NPC236223
0.5469	Remote Similarity	NPC162351
0.5469	Remote Similarity	NPC602125
0.5469	Remote Similarity	NPC609179
0.541	Remote Similarity	NPC293183
0.5397	Remote Similarity	NPC108406
0.5397	Remote Similarity	NPC256283
0.5385	Remote Similarity	NPC223747
0.5385	Remote Similarity	NPC88023
0.5385	Remote Similarity	NPC252933
0.5385	Remote Similarity	NPC111249
0.5385	Remote Similarity	NPC311830
0.5385	Remote Similarity	NPC309025
0.5385	Remote Similarity	NPC604021
0.5366	Remote Similarity	NPC476410
0.5352	Remote Similarity	NPC259757
0.5323	Remote Similarity	NPC219330
0.5323	Remote Similarity	NPC123886
0.5323	Remote Similarity	NPC184536
0.5323	Remote Similarity	NPC156222
0.5323	Remote Similarity	NPC47815
0.5323	Remote Similarity	NPC605617
0.5316	Remote Similarity	NPC203050
0.5316	Remote Similarity	NPC225434
0.5312	Remote Similarity	NPC159103
0.5303	Remote Similarity	NPC483775
0.5286	Remote Similarity	NPC254351
0.5278	Remote Similarity	NPC134796
0.527	Remote Similarity	NPC194593
0.5256	Remote Similarity	NPC101731
0.5238	Remote Similarity	NPC50403
0.5238	Remote Similarity	NPC59951
0.5238	Remote Similarity	NPC241838
0.5238	Remote Similarity	NPC120163
0.5238	Remote Similarity	NPC219927
0.5238	Remote Similarity	NPC610359
0.5238	Remote Similarity	NPC611172
0.5231	Remote Similarity	NPC124784
0.5231	Remote Similarity	NPC195202
0.5231	Remote Similarity	NPC223579
0.5231	Remote Similarity	NPC603596
0.5231	Remote Similarity	NPC604422
0.5231	Remote Similarity	NPC607642
0.5211	Remote Similarity	NPC603692
0.5211	Remote Similarity	NPC610480
0.5161	Remote Similarity	NPC131624
0.5156	Remote Similarity	NPC78913
0.5156	Remote Similarity	NPC162313
0.5156	Remote Similarity	NPC604312
0.5156	Remote Similarity	NPC605047
0.5152	Remote Similarity	NPC78326
0.5128	Remote Similarity	NPC191306
0.5082	Remote Similarity	NPC179271
0.5079	Remote Similarity	NPC127447
0.5079	Remote Similarity	NPC29353
0.5079	Remote Similarity	NPC600177
0.5075	Remote Similarity	NPC227192

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC606283 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5911
0.1-0.2	3162
0.2-0.3	65
0.3-0.4	9
0.4-0.5	1
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
0.6727	Remote Similarity	NPD1511	Phase 2
0.5556	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