NPASS Compound

Natural Product: NPC241829

Natural Product ID	NPC241829
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	JLJAVUZBHSLLJL-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	609882
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans [CHEMONTID:0001604] Tetrahydrofuran lignans [CHEMONTID:0003423] 7,7'-epoxylignans

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 55 57 0 0 0 0 0 0 0 0999 V2000 1.5513 -2.2773 -0.4865 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0248 -1.1432 -1.2922 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1550 -1.5068 -2.1609 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2690 -2.9049 -2.5708 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2715 -0.7991 -1.5358 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9899 -1.3263 -0.4033 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0685 -2.6222 -0.0110 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7967 -3.0285 1.1230 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4611 -2.1160 1.8816 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4009 -0.7907 1.5103 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6901 -0.4157 0.4073 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0997 0.1420 2.3151 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0749 1.5201 1.9615 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1957 -2.4584 3.0086 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3633 -3.7434 3.5165 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6745 0.4326 -1.1318 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5113 0.0267 -0.5046 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3993 1.2213 -0.5476 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8304 2.4991 -0.4271 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5556 3.6469 -0.4436 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9196 3.5307 -0.5867 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5109 2.2778 -0.7073 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7587 1.1262 -0.6888 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8645 2.2253 -0.8442 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5539 1.0020 -0.9717 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6993 4.6737 -0.6109 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1198 5.9411 -0.4962 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3579 -1.8809 0.1929 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7951 -2.8266 0.0756 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0140 -3.0089 -1.2067 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8891 -0.7828 -1.9253 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0550 -0.9130 -3.1366 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3257 -3.1591 -2.8339 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2348 -3.6684 -1.9454 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2582 -3.0333 -3.5786 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0053 -0.4707 -2.3324 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5827 -3.4257 -0.5339 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8315 -4.0799 1.3990 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6610 0.6301 0.1429 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7555 1.7789 1.1433 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0646 1.8897 1.7662 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4637 2.0802 2.8604 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4812 -4.3690 3.3071 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2830 -4.1599 3.0109 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5658 -3.6737 4.6164 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3452 -0.2668 0.5458 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2483 2.5188 -0.3188 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0550 4.5904 -0.3446 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2295 0.1468 -0.7749 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6493 1.1694 -0.8113 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4515 0.5660 -1.9971 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2298 0.3205 -0.1790 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8509 6.7023 -0.8916 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2304 6.0286 -1.1736 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8336 6.1643 0.5623 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 3 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 10 12 1 0 12 13 1 0 9 14 1 0 14 15 1 0 5 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 22 24 1 0 24 25 1 0 21 26 1 0 26 27 1 0 17 2 1 0 23 18 1 0 11 6 1 0 1 28 1 0 1 29 1 0 1 30 1 0 2 31 1 0 3 32 1 0 4 33 1 0 4 34 1 0 4 35 1 0 5 36 1 0 7 37 1 0 8 38 1 0 11 39 1 0 13 40 1 0 13 41 1 0 13 42 1 0 15 43 1 0 15 44 1 0 15 45 1 0 17 46 1 0 19 47 1 0 20 48 1 0 23 49 1 0 25 50 1 0 25 51 1 0 25 52 1 0 27 53 1 0 27 54 1 0 27 55 1 0 M END

Standard InCHIKey	JLJAVUZBHSLLJL-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C22H28O5/c1-13-14(2)22(16-8-10-18(24-4)20(12-16)26-6)27-21(13)15-7-9-17(23-3)19(11-15)25-5/h7-14,21-22H,1-6H3
SMILES	CC1C(C)C(c2ccc(c(c2)OC)OC)OC1c1ccc(c(c1)OC)OC

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
NPO10574	Machilus thunbergii	Species	Lauraceae	Eukaryota	n.a.	bark	n.a.	PMID[11045899]
NPO10574	Machilus thunbergii	Species	Lauraceae	Eukaryota	n.a.	bark	n.a.	PMID[19555186]
NPO10574	Machilus thunbergii	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10574	Machilus thunbergii	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10574	Machilus thunbergii	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10574	Machilus thunbergii	Species	Lauraceae	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

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 NPC241829 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	21377
0.1-0.2	25065
0.2-0.3	2976
0.3-0.4	301
0.4-0.5	70
0.5-0.6	36
0.6-0.7	9
0.7-0.8	0
0.8-0.85	3
0.85-0.9	3
0.9-0.95	0
0.95-1	6

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC216929
1.0	High Similarity	NPC312713
1.0	High Similarity	NPC126935
1.0	High Similarity	NPC65933
1.0	High Similarity	NPC57268
1.0	High Similarity	NPC172676
0.8824	High Similarity	NPC50683
0.8824	High Similarity	NPC112571
0.8824	High Similarity	NPC285725
0.8108	Intermediate Similarity	NPC57119
0.8108	Intermediate Similarity	NPC158471
0.8108	Intermediate Similarity	NPC226862
0.7692	Intermediate Similarity	NPC158331
0.75	Intermediate Similarity	NPC136750
0.75	Intermediate Similarity	NPC487684
0.75	Intermediate Similarity	NPC266848
0.7317	Intermediate Similarity	NPC11258
0.7317	Intermediate Similarity	NPC21867
0.7317	Intermediate Similarity	NPC45774
0.7317	Intermediate Similarity	NPC74914
0.7027	Intermediate Similarity	NPC271208
0.7027	Intermediate Similarity	NPC233224
0.7027	Intermediate Similarity	NPC610263
0.6765	Remote Similarity	NPC9891
0.6765	Remote Similarity	NPC88297
0.6765	Remote Similarity	NPC186845
0.6667	Remote Similarity	NPC260842
0.6667	Remote Similarity	NPC93783
0.6667	Remote Similarity	NPC320380
0.6316	Remote Similarity	NPC121783
0.6316	Remote Similarity	NPC34902
0.6316	Remote Similarity	NPC18449
0.5957	Remote Similarity	NPC135777
0.5957	Remote Similarity	NPC7744
0.5833	Remote Similarity	NPC142547
0.5833	Remote Similarity	NPC228469
0.5833	Remote Similarity	NPC488984
0.5833	Remote Similarity	NPC488985
0.5769	Remote Similarity	NPC302506
0.5769	Remote Similarity	NPC241846
0.5769	Remote Similarity	NPC93610
0.575	Remote Similarity	NPC31530
0.5714	Remote Similarity	NPC222127
0.5714	Remote Similarity	NPC82862
0.5682	Remote Similarity	NPC254120
0.561	Remote Similarity	NPC282703
0.561	Remote Similarity	NPC184733
0.561	Remote Similarity	NPC72046
0.561	Remote Similarity	NPC261812
0.561	Remote Similarity	NPC128208
0.561	Remote Similarity	NPC129570
0.561	Remote Similarity	NPC65183
0.561	Remote Similarity	NPC63238
0.561	Remote Similarity	NPC602603
0.5581	Remote Similarity	NPC606146
0.5577	Remote Similarity	NPC179521
0.5556	Remote Similarity	NPC487685
0.5476	Remote Similarity	NPC204215
0.5455	Remote Similarity	NPC470372
0.5435	Remote Similarity	NPC487683
0.5333	Remote Similarity	NPC227160
0.5333	Remote Similarity	NPC82111
0.5333	Remote Similarity	NPC483654
0.5273	Remote Similarity	NPC77861
0.5217	Remote Similarity	NPC488505
0.5208	Remote Similarity	NPC488986
0.5143	Remote Similarity	NPC258425
0.5111	Remote Similarity	NPC175067

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC241829 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3786
0.1-0.2	5031
0.2-0.3	316
0.3-0.4	16
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