NPASS Compound

Natural Product: NPC609386

Natural Product ID	NPC609386
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	WSSNVJXVWRIBQI-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL575075
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 36 38 0 0 0 0 0 0 0 0999 V2000 -3.1918 3.0215 1.1378 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7209 1.8238 0.6714 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9709 0.7089 0.3296 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6055 -0.4253 -0.1220 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8849 -1.5718 -0.4773 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5240 -2.7182 -0.9336 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9302 -2.7152 -1.0370 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5033 -1.5272 -0.3587 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8390 -0.4053 0.0907 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6215 -0.4363 0.1882 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2789 -1.5162 0.7394 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5791 -1.5803 0.8437 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3664 -0.6335 0.4377 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7504 -0.7396 0.5667 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5197 0.3012 0.1149 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9108 0.2042 0.2400 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9460 1.4220 -0.4511 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5752 1.5122 -0.5717 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7678 0.4843 -0.1283 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4009 0.6089 -0.2651 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8472 1.6126 -0.7742 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5959 0.7026 0.4295 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0422 3.6840 1.4270 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4758 2.9320 1.9532 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6975 3.5532 0.2767 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6796 -0.4154 -0.1983 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3041 -3.5750 -1.6097 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2983 -1.8018 -1.5668 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3459 -2.6945 -0.0142 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9074 -2.4066 -0.6280 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6793 -2.3379 1.0965 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1909 -1.6082 1.0051 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4884 0.3321 -0.5918 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5846 2.2389 -0.8036 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0878 2.3808 -1.0128 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0778 1.5849 0.7826 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 1 0 5 8 2 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 15 17 2 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 9 22 2 0 22 3 1 0 20 10 1 0 19 13 1 0 1 23 1 0 1 24 1 0 1 25 1 0 4 26 1 0 7 27 1 0 7 28 1 0 7 29 1 0 8 30 1 0 11 31 1 0 14 32 1 0 16 33 1 0 17 34 1 0 18 35 1 0 22 36 1 0 M END

Standard InCHIKey	WSSNVJXVWRIBQI-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C17H14O5/c1-20-12-5-10(6-13(8-12)21-2)15-9-22-16-7-11(18)3-4-14(16)17(15)19/h3-9,18H,1-2H3
SMILES	COc1cc(OC)cc(-c2coc3cc(O)ccc3c2=O)c1

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
NPO15836	Astragalus peregrinus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15836	Astragalus peregrinus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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

Activity Type	# Activity
FC	6
EC50	7
Activity	3

Activity Type	# Activity
Individual protein	13
Cell line	3

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT106	Individual protein	Peroxisome proliferator-activated receptor delta	Homo sapiens	FC	=	34.9	n.a.	PMID[23265844]
NPT106	Individual protein	Peroxisome proliferator-activated receptor delta	Homo sapiens	EC50	=	17170.0	nM	PMID[23265844]
NPT106	Individual protein	Peroxisome proliferator-activated receptor delta	Homo sapiens	FC	=	17.5	n.a.	PMID[23265844]
NPT866	Individual protein	Peroxisome proliferator-activated receptor alpha	Homo sapiens	EC50	=	24550.0	nM	PMID[26616289]
NPT866	Individual protein	Peroxisome proliferator-activated receptor alpha	Homo sapiens	FC	=	4.8	n.a.	PMID[19807106]
NPT866	Individual protein	Peroxisome proliferator-activated receptor alpha	Homo sapiens	FC	=	25.3	n.a.	PMID[19807106]
NPT866	Individual protein	Peroxisome proliferator-activated receptor alpha	Homo sapiens	EC50	=	24550.0	nM	PMID[19807106]
NPT866	Individual protein	Peroxisome proliferator-activated receptor alpha	Homo sapiens	EC50	=	24550.0	nM	PMID[23265844]
NPT99	Individual protein	Peroxisome proliferator-activated receptor gamma	Homo sapiens	EC50	=	18860.0	nM	PMID[23265844]
NPT99	Individual protein	Peroxisome proliferator-activated receptor gamma	Homo sapiens	EC50	=	18860.0	nM	PMID[26616289]
NPT99	Individual protein	Peroxisome proliferator-activated receptor gamma	Homo sapiens	FC	=	116.3	n.a.	PMID[19807106]
NPT99	Individual protein	Peroxisome proliferator-activated receptor gamma	Homo sapiens	EC50	=	18860.0	nM	PMID[19807106]
NPT99	Individual protein	Peroxisome proliferator-activated receptor gamma	Homo sapiens	FC	=	11.9	n.a.	PMID[19807106]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT71	Cell line	HEK293	Homo sapiens	Activity	=	80.0	%	PMID[23265844]
NPT71	Cell line	HEK293	Homo sapiens	Activity	>	80.0	%	PMID[19807106]
NPT71	Cell line	HEK293	Homo sapiens	Activity	>	67.0	%	PMID[19807106]

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 NPC609386 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	28190
0.1-0.2	18385
0.2-0.3	2700
0.3-0.4	419
0.4-0.5	99
0.5-0.6	35
0.6-0.7	15
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
0.8077	Intermediate Similarity	NPC203747
0.7963	Intermediate Similarity	NPC191741
0.7736	Intermediate Similarity	NPC209560
0.7736	Intermediate Similarity	NPC490700
0.7455	Intermediate Similarity	NPC262623
0.7455	Intermediate Similarity	NPC12377
0.7321	Intermediate Similarity	NPC139364
0.7018	Intermediate Similarity	NPC80710
0.6897	Remote Similarity	NPC55162
0.6731	Remote Similarity	NPC234560
0.6724	Remote Similarity	NPC12175
0.6724	Remote Similarity	NPC40290
0.6724	Remote Similarity	NPC156953
0.6604	Remote Similarity	NPC212767
0.6557	Remote Similarity	NPC215375
0.6508	Remote Similarity	NPC611071
0.65	Remote Similarity	NPC35544
0.6481	Remote Similarity	NPC242893
0.6441	Remote Similarity	NPC195763
0.6333	Remote Similarity	NPC200060
0.6333	Remote Similarity	NPC291802
0.614	Remote Similarity	NPC487215
0.6061	Remote Similarity	NPC149875
0.5942	Remote Similarity	NPC605730
0.5932	Remote Similarity	NPC181124
0.5806	Remote Similarity	NPC134726
0.5789	Remote Similarity	NPC235428
0.5667	Remote Similarity	NPC69430
0.5667	Remote Similarity	NPC100971
0.5507	Remote Similarity	NPC104555
0.55	Remote Similarity	NPC10467
0.55	Remote Similarity	NPC78341
0.5467	Remote Similarity	NPC488566
0.5455	Remote Similarity	NPC215311
0.5455	Remote Similarity	NPC607759
0.5429	Remote Similarity	NPC104406
0.5429	Remote Similarity	NPC285623
0.5429	Remote Similarity	NPC108859
0.541	Remote Similarity	NPC121522
0.5352	Remote Similarity	NPC223701
0.5352	Remote Similarity	NPC472583
0.5352	Remote Similarity	NPC7989
0.5342	Remote Similarity	NPC258035
0.5333	Remote Similarity	NPC605229
0.5246	Remote Similarity	NPC7013
0.5238	Remote Similarity	NPC264289
0.5161	Remote Similarity	NPC162680
0.5161	Remote Similarity	NPC294409
0.5161	Remote Similarity	NPC490701
0.5161	Remote Similarity	NPC610981
0.5143	Remote Similarity	NPC266572
0.5085	Remote Similarity	NPC182428
0.5082	Remote Similarity	NPC185607
0.5079	Remote Similarity	NPC181209
0.5079	Remote Similarity	NPC239363
0.5077	Remote Similarity	NPC254702
0.5077	Remote Similarity	NPC109187
0.5075	Remote Similarity	NPC161124

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC609386 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4706
0.1-0.2	4345
0.2-0.3	89
0.3-0.4	7
0.4-0.5	3
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