NPASS Compound

Natural Product: NPC107369

Natural Product ID	NPC107369
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	LDENFUOBLMHVHK-LSDHHAIUSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	10093337
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans [CHEMONTID:0001604] Tetrahydrofuran lignans [CHEMONTID:0003424] 9,9'-epoxylignans [CHEMONTID:0001613] Dibenzylbutyrolactone lignans

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 54 57 0 0 0 0 0 0 0 0999 V2000 4.3865 1.5251 3.3732 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9294 1.0725 2.1711 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1837 0.6502 1.0874 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7961 0.6657 1.1705 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0156 0.2550 0.1196 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5626 0.2563 0.2108 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0877 -1.0159 0.6289 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5968 -0.7710 0.6572 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2178 -0.6151 -0.6686 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6546 -0.3704 -0.5461 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1308 0.9218 -0.5577 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4668 1.2356 -0.4171 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3730 0.2215 -0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9366 -1.0760 -0.2415 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5639 -1.3686 -0.3881 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2171 -2.6934 -0.3652 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6234 0.8233 -0.1418 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5007 2.2167 -0.3463 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1203 2.4637 -0.4047 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0127 -1.9724 1.4678 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0491 -1.8934 2.5375 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1446 -1.4010 2.0300 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1914 -1.3414 2.7421 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6171 -0.1895 -1.0642 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9930 -0.2165 -1.1776 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7474 0.2082 -0.0878 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1227 0.1878 -0.1835 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7427 1.3811 -0.6829 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6800 -0.6353 -2.2967 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1063 -1.0953 -3.4850 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7653 0.7257 3.8233 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2232 1.8258 4.0602 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7694 2.4344 3.1414 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3004 1.0128 2.0627 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2680 1.0266 0.9807 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1645 0.6491 -0.7359 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0955 -1.8558 -0.0794 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7341 0.1306 1.2976 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6955 0.1731 -1.2577 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0105 -1.5543 -1.2724 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4162 1.7198 -0.6833 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6621 -1.8666 -0.1153 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4578 -3.3303 0.3827 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9682 2.8130 0.4689 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9916 2.5496 -1.2929 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0176 -1.7971 1.8786 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9238 -2.9291 0.9474 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0144 -0.5129 -1.8921 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4490 1.5908 -1.7283 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3020 2.2019 -0.0490 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8229 1.3979 -0.5051 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5777 -2.1000 -3.6920 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4247 -0.4704 -4.3695 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0327 -1.2636 -3.4698 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 7 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 13 17 1 0 17 18 1 0 18 19 1 0 8 20 1 0 20 21 1 0 21 22 1 0 22 23 2 0 5 24 2 0 24 25 1 0 25 26 2 0 26 27 1 0 27 28 1 0 25 29 1 0 29 30 1 0 26 3 1 0 22 7 1 0 15 10 1 0 19 12 1 0 1 31 1 0 1 32 1 0 1 33 1 0 4 34 1 0 6 35 1 0 6 36 1 0 7 37 1 6 8 38 1 1 9 39 1 0 9 40 1 0 11 41 1 0 14 42 1 0 16 43 1 0 18 44 1 0 18 45 1 0 20 46 1 0 20 47 1 0 24 48 1 0 28 49 1 0 28 50 1 0 28 51 1 0 30 52 1 0 30 53 1 0 30 54 1 0 M END

Standard InCHIKey	LDENFUOBLMHVHK-LSDHHAIUSA-N
Standard InCHI	InChI=1S/C22H24O8/c1-25-19-5-12(6-20(26-2)21(19)27-3)4-15-14(10-28-22(15)24)7-13-8-17-18(9-16(13)23)30-11-29-17/h5-6,8-9,14-15,23H,4,7,10-11H2,1-3H3/t14-,15+/m0/s1
SMILES	COc1cc(C[C@@H]2[C@@H](Cc3cc4c(cc3O)OCO4)COC2=O)cc(c1OC)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
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[10230514]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12956064]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25608854]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	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 NPC107369 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	21642
0.1-0.2	24629
0.2-0.3	3178
0.3-0.4	289
0.4-0.5	73
0.5-0.6	27
0.6-0.7	14
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	Natural Product ID
0.7407	Intermediate Similarity	NPC40237
0.7222	Intermediate Similarity	NPC92693
0.7193	Intermediate Similarity	NPC176586
0.7193	Intermediate Similarity	NPC210354
0.7119	Intermediate Similarity	NPC293757
0.7119	Intermediate Similarity	NPC668
0.678	Remote Similarity	NPC191158
0.678	Remote Similarity	NPC177644
0.6731	Remote Similarity	NPC72796
0.6613	Remote Similarity	NPC145569
0.6562	Remote Similarity	NPC174512
0.6562	Remote Similarity	NPC216223
0.6271	Remote Similarity	NPC205915
0.6154	Remote Similarity	NPC282291
0.6154	Remote Similarity	NPC166137
0.614	Remote Similarity	NPC110958
0.614	Remote Similarity	NPC19890
0.6129	Remote Similarity	NPC106920
0.6129	Remote Similarity	NPC15811
0.6034	Remote Similarity	NPC211386
0.5667	Remote Similarity	NPC143895
0.5522	Remote Similarity	NPC76687
0.5517	Remote Similarity	NPC11453
0.5362	Remote Similarity	NPC136757
0.5345	Remote Similarity	NPC223807
0.5294	Remote Similarity	NPC56184
0.5294	Remote Similarity	NPC482889
0.5263	Remote Similarity	NPC197166
0.5217	Remote Similarity	NPC601255
0.5161	Remote Similarity	NPC68779
0.5161	Remote Similarity	NPC108598
0.5152	Remote Similarity	NPC5310
0.5152	Remote Similarity	NPC300776
0.5152	Remote Similarity	NPC176814
0.5152	Remote Similarity	NPC4982
0.5152	Remote Similarity	NPC606629
0.5091	Remote Similarity	NPC9068
0.5091	Remote Similarity	NPC485484
0.5082	Remote Similarity	NPC192255
0.5082	Remote Similarity	NPC474288
0.5082	Remote Similarity	NPC485480
0.5077	Remote Similarity	NPC273657
0.5075	Remote Similarity	NPC80230
0.5075	Remote Similarity	NPC104024
0.5075	Remote Similarity	NPC101755
0.5075	Remote Similarity	NPC304687
0.5075	Remote Similarity	NPC65574

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC107369 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4472
0.1-0.2	4537
0.2-0.3	130
0.3-0.4	8
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