NPASS Compound

Natural Product: NPC609376

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 40 41 0 0 0 0 0 0 0 0999 V2000 7.1989 0.6616 0.2281 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7890 0.6982 0.1117 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9692 -0.3678 0.3674 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4658 -1.4596 0.7291 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5265 -0.2550 0.2260 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9208 0.9169 -0.1678 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5496 1.0344 -0.3052 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7292 -0.0306 -0.0500 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6222 -0.0421 -0.1476 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4857 0.9687 -0.5126 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.3380 1.2563 0.5181 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2586 0.3031 0.8260 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7376 -0.7375 1.8152 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7754 -1.6486 2.0418 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9186 -0.3614 -0.3332 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.9981 0.4457 -0.7595 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0435 -0.6147 -1.5039 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2525 -1.7341 -1.4165 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2563 0.6444 -1.7964 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1841 1.6683 -2.0048 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3443 -1.2242 0.3509 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7041 -1.3296 0.4839 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6864 0.5115 -0.7494 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5087 1.6063 0.7253 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5162 -0.1651 0.9228 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5697 1.7672 -0.3721 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0999 1.9678 -0.6164 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9340 1.9244 -0.7555 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0834 0.8261 1.3996 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8071 -1.1996 1.5011 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5431 -0.2569 2.8123 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3221 -1.3992 2.8214 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4091 -1.2960 0.0546 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0851 1.2599 -0.2203 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7143 -0.7648 -2.4012 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3279 -2.2466 -0.5947 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5567 0.5141 -2.6203 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7809 2.5622 -1.9784 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7287 -2.1110 0.5685 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1275 -2.2926 0.8019 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 3 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 12 15 1 0 15 16 1 0 15 17 1 0 17 18 1 0 17 19 1 0 19 20 1 0 8 21 1 0 21 22 2 0 22 5 1 0 19 10 1 0 1 23 1 0 1 24 1 0 1 25 1 0 6 26 1 0 7 27 1 0 10 28 1 6 12 29 1 1 13 30 1 0 13 31 1 0 14 32 1 0 15 33 1 1 16 34 1 0 17 35 1 6 18 36 1 0 19 37 1 6 20 38 1 0 21 39 1 0 22 40 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 NPC609376 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	15992
0.1-0.2	29334
0.2-0.3	3363
0.3-0.4	766
0.4-0.5	306
0.5-0.6	67
0.6-0.7	14
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8261	Intermediate Similarity	NPC80098
0.7333	Intermediate Similarity	NPC212729
0.7333	Intermediate Similarity	NPC604498
0.72	Intermediate Similarity	NPC310661
0.7174	Intermediate Similarity	NPC269242
0.7021	Intermediate Similarity	NPC294470
0.6735	Remote Similarity	NPC60589
0.6735	Remote Similarity	NPC469708
0.66	Remote Similarity	NPC200092
0.6364	Remote Similarity	NPC105827
0.6296	Remote Similarity	NPC604356
0.625	Remote Similarity	NPC142319
0.6111	Remote Similarity	NPC218685
0.6087	Remote Similarity	NPC228907
0.6078	Remote Similarity	NPC604439
0.6	Remote Similarity	NPC251102
0.6	Remote Similarity	NPC153149
0.6	Remote Similarity	NPC479028
0.6	Remote Similarity	NPC210298
0.6	Remote Similarity	NPC479031
0.5918	Remote Similarity	NPC276195
0.5893	Remote Similarity	NPC26080
0.5893	Remote Similarity	NPC165686
0.5882	Remote Similarity	NPC25817
0.58	Remote Similarity	NPC217854
0.5741	Remote Similarity	NPC166040
0.569	Remote Similarity	NPC599943
0.5686	Remote Similarity	NPC192810
0.566	Remote Similarity	NPC226712
0.566	Remote Similarity	NPC608788
0.5556	Remote Similarity	NPC221090
0.5556	Remote Similarity	NPC145900
0.5517	Remote Similarity	NPC609351
0.5472	Remote Similarity	NPC299144
0.5455	Remote Similarity	NPC214454
0.5439	Remote Similarity	NPC472024
0.5439	Remote Similarity	NPC270849
0.5439	Remote Similarity	NPC23084
0.5439	Remote Similarity	NPC606892
0.541	Remote Similarity	NPC294166
0.541	Remote Similarity	NPC115022
0.5397	Remote Similarity	NPC248119
0.5397	Remote Similarity	NPC175275
0.537	Remote Similarity	NPC12308
0.5357	Remote Similarity	NPC9912
0.5345	Remote Similarity	NPC26653
0.5345	Remote Similarity	NPC80600
0.5333	Remote Similarity	NPC607971
0.5333	Remote Similarity	NPC609355
0.5323	Remote Similarity	NPC479030
0.5312	Remote Similarity	NPC295970
0.5283	Remote Similarity	NPC9248
0.5283	Remote Similarity	NPC152722
0.5273	Remote Similarity	NPC69513
0.5254	Remote Similarity	NPC248355
0.5254	Remote Similarity	NPC479029
0.5246	Remote Similarity	NPC603686
0.5231	Remote Similarity	NPC92054
0.5231	Remote Similarity	NPC601944
0.5192	Remote Similarity	NPC484157
0.5185	Remote Similarity	NPC198798
0.5179	Remote Similarity	NPC48863
0.5179	Remote Similarity	NPC166168
0.5179	Remote Similarity	NPC251981
0.5179	Remote Similarity	NPC13745
0.5172	Remote Similarity	NPC205054
0.5172	Remote Similarity	NPC19470
0.5167	Remote Similarity	NPC222455
0.5167	Remote Similarity	NPC55040
0.5156	Remote Similarity	NPC210192
0.5156	Remote Similarity	NPC189115
0.5152	Remote Similarity	NPC604833
0.5091	Remote Similarity	NPC36434
0.5088	Remote Similarity	NPC40377
0.5088	Remote Similarity	NPC215833
0.5085	Remote Similarity	NPC214910
0.5085	Remote Similarity	NPC164599
0.5085	Remote Similarity	NPC481303
0.5085	Remote Similarity	NPC210478
0.5082	Remote Similarity	NPC302378
0.5082	Remote Similarity	NPC247146
0.5082	Remote Similarity	NPC34456
0.5079	Remote Similarity	NPC37468
0.5079	Remote Similarity	NPC8497
0.5077	Remote Similarity	NPC264381
0.5077	Remote Similarity	NPC259767
0.5075	Remote Similarity	NPC191046

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC609376 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3723
0.1-0.2	5182
0.2-0.3	217
0.3-0.4	26
0.4-0.5	1
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
0.566	Remote Similarity	NPD1091	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