NPASS Compound

Natural Product: NPC609689

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 33 35 0 0 0 0 0 0 0 0999 V2000 6.3007 0.1788 -0.1572 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3754 -0.8557 -0.4270 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0113 -0.5399 -0.2775 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0975 -1.5457 -0.5391 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7669 -1.2856 -0.4076 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3249 -0.0198 -0.0134 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1076 0.2421 0.1228 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5960 1.4608 0.5048 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9720 1.7053 0.6335 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4122 2.8204 0.9828 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8001 0.6338 0.3489 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1646 0.7722 0.4457 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6747 1.9983 0.8308 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9998 -0.2849 0.1657 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5125 -1.5162 -0.2200 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3735 -2.5811 -0.5013 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1432 -1.6431 -0.3136 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2808 -0.5847 -0.0342 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9862 -0.7096 -0.1241 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2247 0.9726 0.2448 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5942 0.7030 0.1089 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9876 1.0695 -0.7596 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2223 0.4554 0.9216 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3301 -0.1206 -0.4175 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4059 -2.5267 -0.8432 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9933 -2.0161 -0.5932 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0661 2.3003 0.7272 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8742 2.6762 0.0911 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0922 -0.1803 0.2413 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2226 -2.4398 -1.0229 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7553 -2.6063 -0.6155 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9596 1.9718 0.5526 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3071 1.4957 0.3154 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 2 0 18 19 1 0 6 20 1 0 20 21 2 0 21 3 1 0 19 7 1 0 18 11 1 0 1 22 1 0 1 23 1 0 1 24 1 0 4 25 1 0 5 26 1 0 8 27 1 0 13 28 1 0 14 29 1 0 16 30 1 0 17 31 1 0 20 32 1 0 21 33 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 NPC609689 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	27784
0.1-0.2	18235
0.2-0.3	2514
0.3-0.4	860
0.4-0.5	290
0.5-0.6	119
0.6-0.7	29
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	NPC231772
0.7925	Intermediate Similarity	NPC52005
0.7925	Intermediate Similarity	NPC12200
0.7692	Intermediate Similarity	NPC483773
0.7541	Intermediate Similarity	NPC150908
0.7419	Intermediate Similarity	NPC303485
0.7358	Intermediate Similarity	NPC62536
0.7358	Intermediate Similarity	NPC120464
0.7358	Intermediate Similarity	NPC601901
0.7302	Intermediate Similarity	NPC186227
0.72	Intermediate Similarity	NPC50898
0.72	Intermediate Similarity	NPC78540
0.717	Intermediate Similarity	NPC156222
0.717	Intermediate Similarity	NPC29353
0.7167	Intermediate Similarity	NPC183
0.7143	Intermediate Similarity	NPC183950
0.7077	Intermediate Similarity	NPC601565
0.7037	Intermediate Similarity	NPC184136
0.7037	Intermediate Similarity	NPC59951
0.7037	Intermediate Similarity	NPC241838
0.6964	Remote Similarity	NPC606638
0.6909	Remote Similarity	NPC603662
0.6897	Remote Similarity	NPC605634
0.6875	Remote Similarity	NPC72425
0.6852	Remote Similarity	NPC600177
0.6727	Remote Similarity	NPC266597
0.6615	Remote Similarity	NPC71061
0.6607	Remote Similarity	NPC600900
0.6604	Remote Similarity	NPC279121
0.6515	Remote Similarity	NPC272064
0.6429	Remote Similarity	NPC57030
0.6429	Remote Similarity	NPC145379
0.6418	Remote Similarity	NPC215203
0.6418	Remote Similarity	NPC143851
0.6415	Remote Similarity	NPC175013
0.6349	Remote Similarity	NPC196179
0.629	Remote Similarity	NPC112954
0.625	Remote Similarity	NPC52611
0.6212	Remote Similarity	NPC600972
0.6167	Remote Similarity	NPC295036
0.614	Remote Similarity	NPC176775
0.614	Remote Similarity	NPC234133
0.614	Remote Similarity	NPC604085
0.6119	Remote Similarity	NPC290830
0.6094	Remote Similarity	NPC34089
0.6061	Remote Similarity	NPC134796
0.6029	Remote Similarity	NPC14606
0.6	Remote Similarity	NPC274121
0.6	Remote Similarity	NPC610914
0.5965	Remote Similarity	NPC274327
0.5965	Remote Similarity	NPC241498
0.5965	Remote Similarity	NPC127447
0.5942	Remote Similarity	NPC121649
0.5932	Remote Similarity	NPC82325
0.5932	Remote Similarity	NPC54394
0.5932	Remote Similarity	NPC159103
0.5893	Remote Similarity	NPC213216
0.5873	Remote Similarity	NPC111112
0.5862	Remote Similarity	NPC22519
0.5862	Remote Similarity	NPC604462
0.5857	Remote Similarity	NPC18699
0.5833	Remote Similarity	NPC195202
0.5833	Remote Similarity	NPC223579
0.5833	Remote Similarity	NPC603596
0.5789	Remote Similarity	NPC293183
0.5789	Remote Similarity	NPC610974
0.5763	Remote Similarity	NPC294409
0.5763	Remote Similarity	NPC256283
0.5763	Remote Similarity	NPC490701
0.5692	Remote Similarity	NPC470402
0.569	Remote Similarity	NPC301323
0.569	Remote Similarity	NPC184536
0.569	Remote Similarity	NPC103342
0.569	Remote Similarity	NPC605617
0.5676	Remote Similarity	NPC88023
0.5676	Remote Similarity	NPC165970
0.5676	Remote Similarity	NPC309025
0.5667	Remote Similarity	NPC255350
0.5634	Remote Similarity	NPC205026
0.5625	Remote Similarity	NPC138299
0.56	Remote Similarity	NPC288131
0.5593	Remote Similarity	NPC286342
0.5588	Remote Similarity	NPC248739
0.5571	Remote Similarity	NPC63454
0.5571	Remote Similarity	NPC183851
0.5556	Remote Similarity	NPC265624
0.5538	Remote Similarity	NPC301217
0.5536	Remote Similarity	NPC604293
0.5517	Remote Similarity	NPC131624
0.5507	Remote Similarity	NPC601984
0.55	Remote Similarity	NPC108406
0.5484	Remote Similarity	NPC279668
0.5439	Remote Similarity	NPC101294
0.5439	Remote Similarity	NPC2771
0.5429	Remote Similarity	NPC158027
0.5424	Remote Similarity	NPC219330
0.5424	Remote Similarity	NPC123886
0.5424	Remote Similarity	NPC47815
0.5424	Remote Similarity	NPC194281
0.5405	Remote Similarity	NPC191306
0.5405	Remote Similarity	NPC55443
0.5385	Remote Similarity	NPC113163
0.5373	Remote Similarity	NPC254351
0.5352	Remote Similarity	NPC194593
0.5345	Remote Similarity	NPC14958
0.5333	Remote Similarity	NPC100887
0.5333	Remote Similarity	NPC33265
0.5333	Remote Similarity	NPC50403
0.5333	Remote Similarity	NPC201451
0.5333	Remote Similarity	NPC48479
0.5333	Remote Similarity	NPC198826
0.5333	Remote Similarity	NPC28274
0.5333	Remote Similarity	NPC250266
0.5333	Remote Similarity	NPC120163
0.5333	Remote Similarity	NPC610359
0.5323	Remote Similarity	NPC124784
0.5323	Remote Similarity	NPC287101
0.5323	Remote Similarity	NPC162351
0.5323	Remote Similarity	NPC604422
0.5323	Remote Similarity	NPC607642
0.5323	Remote Similarity	NPC609179
0.5316	Remote Similarity	NPC66618
0.5316	Remote Similarity	NPC305987
0.5303	Remote Similarity	NPC291746
0.5294	Remote Similarity	NPC603692
0.5246	Remote Similarity	NPC78913
0.5244	Remote Similarity	NPC477628
0.5238	Remote Similarity	NPC133953
0.5238	Remote Similarity	NPC125062
0.5238	Remote Similarity	NPC278323
0.5238	Remote Similarity	NPC279989
0.5238	Remote Similarity	NPC137062
0.5217	Remote Similarity	NPC259757
0.5211	Remote Similarity	NPC600396
0.5205	Remote Similarity	NPC95090
0.5205	Remote Similarity	NPC27408
0.5167	Remote Similarity	NPC203891
0.5167	Remote Similarity	NPC284552
0.5167	Remote Similarity	NPC44079
0.5167	Remote Similarity	NPC275722
0.5167	Remote Similarity	NPC125887
0.5167	Remote Similarity	NPC239128
0.5161	Remote Similarity	NPC69394
0.5161	Remote Similarity	NPC212678
0.5161	Remote Similarity	NPC83508
0.5156	Remote Similarity	NPC67322
0.5156	Remote Similarity	NPC483775
0.5139	Remote Similarity	NPC159707
0.5135	Remote Similarity	NPC181712
0.5132	Remote Similarity	NPC101731
0.5132	Remote Similarity	NPC80188
0.5128	Remote Similarity	NPC4390
0.5128	Remote Similarity	NPC600989
0.5082	Remote Similarity	NPC18260
0.5082	Remote Similarity	NPC281207
0.5082	Remote Similarity	NPC231018
0.5082	Remote Similarity	NPC188203
0.5082	Remote Similarity	NPC610380
0.5079	Remote Similarity	NPC177298
0.5079	Remote Similarity	NPC160951
0.5079	Remote Similarity	NPC283600
0.5075	Remote Similarity	NPC288840
0.5072	Remote Similarity	NPC224714
0.5072	Remote Similarity	NPC610480
0.5067	Remote Similarity	NPC472459
0.5065	Remote Similarity	NPC172202
0.5065	Remote Similarity	NPC284127
0.5059	Remote Similarity	NPC477629

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC609689 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4926
0.1-0.2	4091
0.2-0.3	119
0.3-0.4	9
0.4-0.5	3
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
0.6604	Remote Similarity	NPD1511	Phase 2
0.5667	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