NPASS Compound

Natural Product: NPC257942

Natural Product ID	NPC257942
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ZNAQRFWUMXTQHU-IWLKZTELSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	101618866
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0003782] Kaurane diterpenoids

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 68 0 0 0 0 0 0 0 0999 V2000 5.9947 -2.8308 1.0425 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9701 -1.7338 1.1735 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2562 -1.4532 0.1211 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2455 -0.4170 0.1416 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0245 0.2474 1.1809 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4846 -0.1338 -1.0174 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5354 0.8686 -0.9288 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7883 1.9572 -1.8969 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7936 2.8106 -1.8631 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7085 1.9054 -2.8989 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4330 2.8188 -2.5272 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9928 2.5917 -1.1795 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8095 1.2559 -0.5759 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.1483 0.6130 -0.1701 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.1117 0.5797 -1.2958 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7117 1.5440 0.9016 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3915 1.0669 2.2786 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9308 -0.2881 2.5975 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7711 -1.2655 1.4336 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1515 -2.5427 2.0090 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8073 -0.6713 0.4832 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2522 -1.6426 -0.5373 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0963 -1.0823 -0.9384 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1218 0.3459 -1.2808 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1684 0.4929 -2.7829 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0895 -1.6288 0.9424 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4311 -2.8448 0.8675 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0528 -0.7218 0.5311 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8045 -1.0291 2.4420 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9118 -2.4427 1.5384 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2149 -3.0368 -0.0124 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6342 -3.7591 1.5020 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4212 -2.0185 -0.8190 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5267 1.3048 0.0807 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8797 3.5773 -2.6353 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5222 2.7418 -1.0706 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0225 2.1552 -3.9138 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1950 2.7017 -3.3549 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0585 3.8577 -2.6487 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1058 2.7897 -1.2368 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6337 3.4369 -0.5175 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3437 1.4342 0.4484 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0329 1.1935 -1.0714 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4492 -0.3917 -1.6445 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7053 1.1017 -2.2006 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7995 1.6997 0.7963 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2691 2.5751 0.8099 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8565 1.7872 2.9914 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2874 1.1418 2.4849 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9797 -0.2707 2.9580 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3247 -0.6827 3.4353 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4414 -3.3759 1.3392 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0801 -2.4481 2.1754 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6538 -2.7201 2.9816 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8903 -0.4325 1.1287 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9184 -1.7807 -1.4059 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1210 -2.6116 -0.0576 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4160 -1.6895 -1.8282 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7961 -1.3041 -0.0916 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9800 -0.2015 -3.1216 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7690 0.3151 -3.2950 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6331 -0.8818 -0.2893 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0007 0.0443 2.2950 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7738 -1.1574 2.8091 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5405 -1.4648 3.1867 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 3 3 4 1 0 4 5 2 0 4 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 6 14 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 1 19 21 1 0 21 22 1 0 22 23 1 0 24 23 1 6 24 25 1 0 19 26 1 0 26 27 2 0 26 28 1 0 2 29 1 0 24 7 1 0 25 10 1 0 24 13 1 0 21 14 1 0 1 30 1 0 1 31 1 0 1 32 1 0 3 33 1 0 7 34 1 1 9 35 1 0 9 36 1 0 10 37 1 6 11 38 1 0 11 39 1 0 12 40 1 0 12 41 1 0 13 42 1 1 15 43 1 0 15 44 1 0 15 45 1 0 16 46 1 0 16 47 1 0 17 48 1 0 17 49 1 0 18 50 1 0 18 51 1 0 20 52 1 0 20 53 1 0 20 54 1 0 21 55 1 1 22 56 1 0 22 57 1 0 23 58 1 0 23 59 1 0 25 60 1 0 25 61 1 0 28 62 1 0 29 63 1 0 29 64 1 0 29 65 1 0 M END

Standard InCHIKey	ZNAQRFWUMXTQHU-IWLKZTELSA-N
Standard InCHI	InChI=1S/C25H36O4/c1-15(2)13-20(26)29-21-16(3)17-7-8-19-23(4)10-6-11-24(5,22(27)28)18(23)9-12-25(19,21)14-17/h13,17-19,21H,3,6-12,14H2,1-2,4-5H3,(H,27,28)/t17-,18+,19+,21+,23-,24-,25-/m1/s1
SMILES	CC(=CC(=O)O[C@H]1C(=C)[C@@H]2CC[C@H]3[C@]4(C)CCC[C@](C)([C@H]4CC[C@]13C2)C(=O)O)C

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
NPO40042	Baccharis lateralis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33236902]
NPO14173	Ipomoea reptans	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1402	Adenocarpus foliolosus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO29061	Anthoxanthum nitens	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11975	Antillogorgia elisabethae	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO6564	Betula exilis	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13183	Cereus dumortieri	Species	Sagartiidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7550	Chromolaena arnottiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22285	Clethra macrophylla	Species	Clethraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10309	Ichthyothere terminalis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13484	Vidalia volubilis	Species	Tephritidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13884	Microglossa pyrrhopappa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10163	Oreoherzogia fallax	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11036	Piper taboganum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO19055	Plenodomus tracheiphilus	Species	Leptosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11508	Polygala reinii	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14374	Retama duriaei	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14581	Rubia schumanniana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3031	Sabal causiarum	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3031	Sabal causiarum	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11508	Polygala reinii	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29061	Anthoxanthum nitens	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19055	Plenodomus tracheiphilus	Species	Leptosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22285	Clethra macrophylla	Species	Clethraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3031	Sabal causiarum	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10309	Ichthyothere terminalis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14374	Retama duriaei	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11036	Piper taboganum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14581	Rubia schumanniana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13884	Microglossa pyrrhopappa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10163	Oreoherzogia fallax	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11975	Antillogorgia elisabethae	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1402	Adenocarpus foliolosus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14173	Ipomoea reptans	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7550	Chromolaena arnottiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11508	Polygala reinii	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13484	Vidalia volubilis	Species	Tephritidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6564	Betula exilis	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13183	Cereus dumortieri	Species	Sagartiidae	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
Activity	5
CC50	2

Activity Type	# Activity
Cell line	2
Organism	5

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
NPT941	Cell line	HaCaT	Homo sapiens	CC50	=	147200.0	nM	PMID[33236902]
NPT519	Cell line	SH-SY5Y	Homo sapiens	CC50	=	106200.0	nM	PMID[33236902]
NPT2254	Organism	Schistosoma mansoni	Schistosoma mansoni	Activity	=	29.8	%	PMID[33236902]
NPT2254	Organism	Schistosoma mansoni	Schistosoma mansoni	Activity	=	23.5	%	PMID[33236902]
NPT2254	Organism	Schistosoma mansoni	Schistosoma mansoni	Activity	=	71.6	%	PMID[33236902]
NPT2254	Organism	Schistosoma mansoni	Schistosoma mansoni	Activity	=	69.2	%	PMID[33236902]
NPT2254	Organism	Schistosoma mansoni	Schistosoma mansoni	Activity	=	61.9	%	PMID[33236902]

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
-	Schistosoma mansoni	LC50	=	11600.0	nM	PMID[33236902]

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 NPC257942 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	16928
0.1-0.2	29345
0.2-0.3	3331
0.3-0.4	173
0.4-0.5	67
0.5-0.6	11
0.6-0.7	1
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
0.8393	Intermediate Similarity	NPC472505
0.6197	Remote Similarity	NPC479782
0.5469	Remote Similarity	NPC600598
0.5397	Remote Similarity	NPC170985
0.5385	Remote Similarity	NPC215893
0.5231	Remote Similarity	NPC170862
0.5152	Remote Similarity	NPC474404
0.5079	Remote Similarity	NPC330659
0.5079	Remote Similarity	NPC244708
0.5079	Remote Similarity	NPC161187
0.5077	Remote Similarity	NPC212661
0.5077	Remote Similarity	NPC471035
0.507	Remote Similarity	NPC475118

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC257942 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5413
0.1-0.2	3678
0.2-0.3	57
0.3-0.4	1
0.4-0.5	1
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