NPASS Compound

Natural Product: NPC248505

Natural Product ID	NPC248505
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(E)-7-(1,3-Benzodioxol-5-Yl)-1-Pyrrolidin-1-Ylhept-2-En-1-One
IUPAC Name	(E)-7-(1,3-benzodioxol-5-yl)-1-pyrrolidin-1-ylhept-2-en-1-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3338702
PubChem CID	10638035
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000296] Benzodioxoles

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 45 47 0 0 0 0 0 0 0 0999 V2000 1.2309 -0.4190 1.3659 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1306 0.4187 1.9700 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1438 -0.3171 1.8306 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1858 0.1436 1.1683 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4023 -0.6476 1.0810 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4487 -1.7666 1.6397 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5016 -0.1239 0.3628 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.5373 1.1553 -0.3121 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0225 1.3732 -0.5921 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4502 -0.0669 -0.9029 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7656 -0.8134 0.2039 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9054 -0.6465 -0.0861 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9535 -1.4795 -0.7815 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2900 -0.8737 -0.7585 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1227 -1.1764 0.2996 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3953 -0.6427 0.3877 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8458 0.1986 -0.5822 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0051 0.4960 -1.6378 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7310 -0.0190 -1.7558 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7186 1.3589 -2.4534 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9307 1.7521 -1.8405 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0610 0.8755 -0.7548 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1790 0.1890 1.4241 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3358 -1.3571 1.9406 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3362 0.7127 3.0107 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0203 1.3651 1.3836 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2107 -1.3005 2.3109 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1052 1.1167 0.6988 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1833 1.9894 0.3255 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9659 1.1216 -1.2755 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2060 2.0521 -1.4211 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5193 1.6426 0.3575 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5497 -0.1759 -0.8799 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0062 -0.3992 -1.8689 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6308 -1.8900 -0.0162 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3430 -0.6473 1.1424 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7626 0.3412 -0.5529 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0503 -1.2157 -0.1446 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6741 -1.7044 -1.8230 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9914 -2.4581 -0.2523 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8170 -1.8455 1.1085 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0462 -0.8878 1.2278 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0766 0.2211 -2.5906 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7361 1.5364 -2.5904 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9323 2.8137 -1.5330 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 5 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 1 12 1 0 12 13 1 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 18 20 1 0 20 21 1 0 21 22 1 0 11 7 1 0 19 14 1 0 22 17 1 0 1 23 1 0 1 24 1 0 2 25 1 0 2 26 1 0 3 27 1 0 4 28 1 0 8 29 1 0 8 30 1 0 9 31 1 0 9 32 1 0 10 33 1 0 10 34 1 0 11 35 1 0 11 36 1 0 12 37 1 0 12 38 1 0 13 39 1 0 13 40 1 0 15 41 1 0 16 42 1 0 19 43 1 0 21 44 1 0 21 45 1 0 M END

Standard InCHIKey	AXDKDWWPOMVARR-XBXARRHUSA-N
Standard InCHI	InChI=1S/C18H23NO3/c20-18(19-11-5-6-12-19)8-4-2-1-3-7-15-9-10-16-17(13-15)22-14-21-16/h4,8-10,13H,1-3,5-7,11-12,14H2/b8-4+
SMILES	C(C/C=C/C(=O)N1CCCC1)CCc1ccc2c(c1)OCO2

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
NPO30128	Piper boehmeriaefolium	Species	Piperaceae	Eukaryota	whole plant	Luxi County, Yunnan Province, China	2008-OCT	PMID[21158422]
NPO30128	Piper boehmeriaefolium	Species	Piperaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[21158422]
NPO30128	Piper boehmeriaefolium	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO30128	Piper boehmeriaefolium	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

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
IC50	8
Ratio IC50	1

Activity Type	# Activity
Cell line	7
Non-molecular	1
Others	1

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
NPT81	Cell line	A549	Homo sapiens	IC50	=	21200.0	nM	PMID[25241925]
NPT83	Cell line	MCF7	Homo sapiens	IC50	>	40000.0	nM	PMID[25241925]
NPT133	Cell line	ZR-75-1	Homo sapiens	IC50	>	40000.0	nM	PMID[25241925]
NPT134	Cell line	SK-BR-3	Homo sapiens	IC50	>	40000.0	nM	PMID[25241925]
NPT82	Cell line	MDA-MB-231	Homo sapiens	IC50	>	40000.0	nM	PMID[25241925]
NPT90	Cell line	DU-145	Homo sapiens	IC50	=	36150.0	nM	PMID[25241925]
NPT91	Cell line	KB	Homo sapiens	IC50	=	31080.0	nM	PMID[25241925]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	=	28250.0	nM	PMID[25241925]
NPT2	Others	Unspecified	n.a.	Ratio IC50	=	1.1	n.a.	PMID[25241925]

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 NPC248505 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	20462
0.1-0.2	27598
0.2-0.3	1540
0.3-0.4	191
0.4-0.5	37
0.5-0.6	19
0.6-0.7	7
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
0.8	Intermediate Similarity	NPC95366
0.7692	Intermediate Similarity	NPC252107
0.7091	Intermediate Similarity	NPC145446
0.7091	Intermediate Similarity	NPC137172
0.6792	Remote Similarity	NPC608515
0.6667	Remote Similarity	NPC605639
0.6379	Remote Similarity	NPC193673
0.6271	Remote Similarity	NPC230698
0.6271	Remote Similarity	NPC99078
0.6271	Remote Similarity	NPC96406
0.6207	Remote Similarity	NPC159150
0.5781	Remote Similarity	NPC270811
0.5781	Remote Similarity	NPC471073
0.5714	Remote Similarity	NPC246974
0.5556	Remote Similarity	NPC328419
0.5469	Remote Similarity	NPC220923
0.5469	Remote Similarity	NPC196609
0.5455	Remote Similarity	NPC147247
0.5424	Remote Similarity	NPC94280
0.5397	Remote Similarity	NPC103947
0.5397	Remote Similarity	NPC45783
0.5333	Remote Similarity	NPC255817
0.5333	Remote Similarity	NPC136330
0.5312	Remote Similarity	NPC73883
0.5312	Remote Similarity	NPC251454
0.5263	Remote Similarity	NPC217574
0.5172	Remote Similarity	NPC167096
0.5172	Remote Similarity	NPC605721
0.5161	Remote Similarity	NPC205178
0.5161	Remote Similarity	NPC227218

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC248505 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3897
0.1-0.2	5069
0.2-0.3	173
0.3-0.4	9
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
0.5333	Remote Similarity	NPD2492	Phase 2

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