NPASS Compound

Natural Product: NPC609880

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 72 74 0 0 0 0 0 0 0 0999 V2000 1.7286 -4.9149 1.0539 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3474 -4.2555 -0.0111 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8259 -2.8867 -0.2277 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7361 -2.3265 0.7909 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4392 -2.2235 -1.3081 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8369 -0.8707 -1.6431 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7043 0.1397 -1.8039 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1743 -0.3852 -2.9179 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3739 1.3905 -2.2921 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7036 1.0793 -3.0109 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6988 2.4182 -1.2880 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9660 2.3613 0.0256 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6898 1.6968 0.9714 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3864 1.6848 -0.1332 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1329 1.6786 1.1623 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6871 0.6159 1.6334 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7021 -0.7384 1.0114 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1623 -1.7075 1.8368 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9481 -2.7454 2.3644 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1832 -2.7225 2.0162 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4650 -3.7898 3.2392 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2105 -3.8113 3.6018 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3878 -4.8369 3.7274 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2229 -0.6939 -0.4172 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1273 0.3314 -0.5718 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0915 3.1305 1.4886 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1195 3.4834 2.3566 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6003 4.1628 3.4869 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0590 3.7440 0.2190 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2788 2.6780 -0.7343 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0357 3.2389 -1.9490 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9991 3.4997 -2.8805 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5790 4.1222 -4.1822 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1811 3.2245 -2.6440 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3867 -4.4804 1.7810 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3907 -5.9249 1.2116 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6811 -4.6812 -0.7525 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9478 -1.2682 0.7420 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2345 -2.4791 1.7955 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6814 -2.9491 0.8439 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7684 -2.7659 -1.9964 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5970 -0.4853 -0.9541 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3909 -0.9607 -2.6314 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9480 0.3546 -3.2139 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5046 -0.4720 -3.8182 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5597 -1.3881 -2.7430 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7705 1.7951 -3.1563 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1522 2.0723 -3.3513 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4613 0.7012 -2.3044 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5690 0.5241 -3.9351 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5554 3.4231 -1.7864 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7920 2.4261 -1.0193 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7847 3.4072 0.3069 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2051 1.2245 1.6677 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2077 0.7159 2.6046 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8132 -0.9858 0.8983 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1424 -4.5889 4.2507 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4968 -3.0646 3.2745 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2559 -5.0188 4.8318 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4558 -4.5388 3.6335 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2197 -5.8241 3.2523 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8207 -1.7062 -0.6104 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0431 -0.5343 -1.1530 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6041 -0.0499 0.2503 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0558 3.4917 1.9275 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1021 5.0747 3.1205 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1861 4.3449 4.2197 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3674 3.5021 3.9415 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3638 2.4720 -0.6296 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6047 3.3860 -5.0055 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2573 4.9854 -4.3413 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5445 4.4934 -4.1220 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 0 3 5 2 0 5 6 1 0 7 6 1 1 7 8 1 0 7 9 1 0 9 10 1 0 9 11 1 0 11 12 1 0 12 13 1 0 12 14 1 0 14 15 1 1 15 16 2 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 2 0 19 21 1 0 21 22 2 0 21 23 1 0 17 24 1 0 24 25 1 0 15 26 1 0 26 27 1 0 27 28 1 0 26 29 1 0 29 30 1 0 30 31 1 0 31 32 1 0 32 33 1 0 32 34 2 0 25 7 1 0 25 14 1 0 30 14 1 0 1 35 1 0 1 36 1 0 2 37 1 0 4 38 1 0 4 39 1 0 4 40 1 0 5 41 1 0 6 42 1 0 6 43 1 0 8 44 1 0 8 45 1 0 8 46 1 0 9 47 1 6 10 48 1 0 10 49 1 0 10 50 1 0 11 51 1 0 11 52 1 0 12 53 1 1 13 54 1 0 16 55 1 0 17 56 1 6 22 57 1 0 22 58 1 0 23 59 1 0 23 60 1 0 23 61 1 0 24 62 1 0 24 63 1 0 25 64 1 1 26 65 1 1 28 66 1 0 28 67 1 0 28 68 1 0 30 69 1 6 33 70 1 0 33 71 1 0 33 72 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 NPC609880 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	17948
0.1-0.2	27464
0.2-0.3	4294
0.3-0.4	57
0.4-0.5	36
0.5-0.6	17
0.6-0.7	16
0.7-0.8	0
0.8-0.85	7
0.85-0.9	7
0.9-0.95	3
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9322	High Similarity	NPC609711
0.9138	High Similarity	NPC488659
0.9138	High Similarity	NPC604149
0.8689	High Similarity	NPC134270
0.8689	High Similarity	NPC488660
0.8689	High Similarity	NPC488657
0.8689	High Similarity	NPC488654
0.8548	High Similarity	NPC488658
0.8548	High Similarity	NPC488655
0.85	High Similarity	NPC602188
0.8281	Intermediate Similarity	NPC252296
0.8095	Intermediate Similarity	NPC201880
0.8095	Intermediate Similarity	NPC81567
0.8095	Intermediate Similarity	NPC329623
0.8095	Intermediate Similarity	NPC488652
0.8065	Intermediate Similarity	NPC488653
0.8065	Intermediate Similarity	NPC488656
0.7969	Intermediate Similarity	NPC330003
0.7969	Intermediate Similarity	NPC470321
0.7969	Intermediate Similarity	NPC264867
0.7969	Intermediate Similarity	NPC473207
0.7969	Intermediate Similarity	NPC609715
0.7727	Intermediate Similarity	NPC488964
0.7727	Intermediate Similarity	NPC184512
0.68	Remote Similarity	NPC109376
0.6765	Remote Similarity	NPC479491
0.6667	Remote Similarity	NPC238397
0.6571	Remote Similarity	NPC479941
0.6533	Remote Similarity	NPC116292
0.6471	Remote Similarity	NPC479943
0.6389	Remote Similarity	NPC119550
0.6286	Remote Similarity	NPC479940
0.6286	Remote Similarity	NPC7644
0.6286	Remote Similarity	NPC316974
0.6286	Remote Similarity	NPC479497
0.6197	Remote Similarity	NPC475889
0.6197	Remote Similarity	NPC7613
0.6197	Remote Similarity	NPC479942
0.6056	Remote Similarity	NPC311223
0.6027	Remote Similarity	NPC471363
0.5867	Remote Similarity	NPC127933
0.5758	Remote Similarity	NPC604446
0.5714	Remote Similarity	NPC600724
0.5571	Remote Similarity	NPC606965
0.5507	Remote Similarity	NPC603601
0.55	Remote Similarity	NPC179128
0.5366	Remote Similarity	NPC486751
0.5357	Remote Similarity	NPC224660
0.5333	Remote Similarity	NPC218158
0.527	Remote Similarity	NPC473204
0.5227	Remote Similarity	NPC320734
0.5205	Remote Similarity	NPC88507
0.5205	Remote Similarity	NPC488235
0.5181	Remote Similarity	NPC316708
0.5132	Remote Similarity	NPC217921
0.5132	Remote Similarity	NPC135015
0.5122	Remote Similarity	NPC87630

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC609880 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6979
0.1-0.2	2139
0.2-0.3	32
0.3-0.4	0
0.4-0.5	0
0.5-0.6	0
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
		NPD

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