NPASS Compound

Natural Product: NPC609480

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 65 64 0 0 0 0 0 0 0 0999 V2000 8.6957 -1.0100 -2.3000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2555 -1.0787 -2.7550 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3454 -0.7171 -1.5939 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9006 -0.7647 -1.9741 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0566 -0.3870 -0.7950 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2144 -1.2802 0.3885 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3360 -0.8784 1.5168 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5861 0.5180 2.0520 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6915 0.8279 3.1684 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8202 1.8056 3.2209 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6502 2.7387 2.0962 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2257 2.6768 1.5597 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1148 1.3079 1.0758 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5172 1.2129 0.5333 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5680 1.5607 1.5611 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9393 1.4554 0.9891 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3221 0.0990 0.4803 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7114 0.1749 -0.0460 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3558 1.2525 -0.0150 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3615 -0.9230 -0.5914 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6593 -0.9105 -1.0985 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5796 -1.8718 -0.3735 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0633 -3.1649 -0.5096 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5912 -1.2380 -2.5754 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8147 -0.2907 -3.2395 O 0 0 0 0 0 0 0 0 0 0 0 0 8.7766 -1.6346 -1.3885 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3793 -1.3253 -3.0969 H 0 0 0 0 0 0 0 0 0 0 0 0 8.9314 0.0391 -2.0292 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1267 -0.3050 -3.5396 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9912 -2.0810 -3.1266 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5646 0.2994 -1.2223 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5557 -1.4806 -0.7892 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7402 0.0093 -2.7622 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6069 -1.7708 -2.3948 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3142 0.6639 -0.5397 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9693 -0.4476 -1.0946 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2701 -1.3760 0.7320 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8807 -2.2997 0.0647 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2603 -1.0125 1.2075 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4960 -1.5720 2.3764 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5537 1.1882 1.1978 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6298 0.4859 2.4653 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7627 0.1698 4.0497 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1930 1.9337 4.1405 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7127 3.7839 2.5503 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4091 2.7277 1.3333 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4959 2.9957 2.3452 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1601 3.3957 0.7353 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0267 0.5880 1.9195 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5728 1.0470 0.2572 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5807 1.9818 -0.2821 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7080 0.2107 0.0729 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4354 0.9930 2.4983 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4150 2.6544 1.8039 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0173 2.1560 0.1185 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7332 1.7800 1.6890 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3505 -0.6218 1.3241 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6231 -0.3222 -0.2623 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1508 0.0936 -1.0268 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.7289 -1.5872 0.6799 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.5852 -1.8959 -0.8397 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5097 -3.6786 -1.2005 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5979 -1.2186 -3.0566 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2051 -2.2721 -2.7423 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8728 -0.2915 -2.9420 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 18 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 21 24 1 0 24 25 1 0 1 26 1 0 1 27 1 0 1 28 1 0 2 29 1 0 2 30 1 0 3 31 1 0 3 32 1 0 4 33 1 0 4 34 1 0 5 35 1 0 5 36 1 0 6 37 1 0 6 38 1 0 7 39 1 0 7 40 1 0 8 41 1 0 8 42 1 0 9 43 1 0 10 44 1 0 11 45 1 0 11 46 1 0 12 47 1 0 12 48 1 0 13 49 1 0 13 50 1 0 14 51 1 0 14 52 1 0 15 53 1 0 15 54 1 0 16 55 1 0 16 56 1 0 17 57 1 0 17 58 1 0 21 59 1 0 22 60 1 0 22 61 1 0 23 62 1 0 24 63 1 0 24 64 1 0 25 65 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 NPC609480 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	15679
0.1-0.2	29235
0.2-0.3	4147
0.3-0.4	630
0.4-0.5	128
0.5-0.6	22
0.6-0.7	4
0.7-0.8	0
0.8-0.85	4
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC148192
0.8824	High Similarity	NPC476660
0.8286	Intermediate Similarity	NPC81896
0.8286	Intermediate Similarity	NPC476657
0.8286	Intermediate Similarity	NPC476659
0.8065	Intermediate Similarity	NPC23155
0.7568	Intermediate Similarity	NPC476658
0.7	Intermediate Similarity	NPC48218
0.7	Intermediate Similarity	NPC141481
0.7	Intermediate Similarity	NPC464342
0.6512	Remote Similarity	NPC473559
0.6512	Remote Similarity	NPC324981
0.6176	Remote Similarity	NPC309606
0.6154	Remote Similarity	NPC104537
0.5897	Remote Similarity	NPC277597
0.5833	Remote Similarity	NPC128061
0.5714	Remote Similarity	NPC330426
0.5714	Remote Similarity	NPC127091
0.5714	Remote Similarity	NPC22101
0.5676	Remote Similarity	NPC39633
0.5581	Remote Similarity	NPC54925
0.5476	Remote Similarity	NPC475443
0.5476	Remote Similarity	NPC473829
0.5455	Remote Similarity	NPC47363
0.5455	Remote Similarity	NPC287231
0.5405	Remote Similarity	NPC228473
0.5385	Remote Similarity	NPC223677
0.5385	Remote Similarity	NPC28779
0.5143	Remote Similarity	NPC603863
0.5122	Remote Similarity	NPC608765
0.5122	Remote Similarity	NPC609320
0.5116	Remote Similarity	NPC321919
0.5116	Remote Similarity	NPC476654
0.5116	Remote Similarity	NPC476655
0.5116	Remote Similarity	NPC476656
0.5091	Remote Similarity	NPC488689

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC609480 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6092
0.1-0.2	2872
0.2-0.3	151
0.3-0.4	29
0.4-0.5	4
0.5-0.6	2
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
0.55	Remote Similarity	NPD3730	Pre-clinical
0.5455	Remote Similarity	NPD2699	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