NPASS Compound

Natural Product: NPC162720

Natural Product ID	NPC162720
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ORQFDHFZSMXRLM-HZPDHXFCSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	515707
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001969] Dibenzylbutane 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 56 57 0 0 0 0 0 0 0 0999 V2000 -1.0464 -1.5139 -0.6522 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6990 -0.2471 0.0916 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6353 0.8941 -0.2403 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0391 0.5959 0.0927 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5493 0.9012 1.3371 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8622 0.6241 1.6524 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7205 0.0342 0.7481 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1958 -0.2660 -0.4943 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8845 0.0057 -0.8230 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0594 -0.8598 -1.4052 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.6452 -1.2174 -2.7136 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0552 -0.2491 1.0642 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5020 0.0948 2.3618 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7148 0.2025 -0.2032 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9532 0.4856 -1.6546 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6723 -0.8409 0.2897 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0810 -0.4991 0.0504 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7346 -0.8643 -1.1094 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0609 -0.5474 -1.3451 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7834 0.1588 -0.4055 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1472 0.5348 0.7646 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8268 0.2108 0.9823 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8824 1.2491 1.7121 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2353 1.6440 2.9270 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1136 0.5049 -0.5852 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7447 0.1082 -1.7935 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5201 -2.3581 -0.1273 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6624 -1.5272 -1.6917 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1120 -1.7261 -0.5815 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7297 -0.4944 1.1722 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5773 1.1858 -1.2980 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2999 1.7623 0.3637 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9289 1.3726 2.1131 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2889 0.8578 2.6345 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5495 -0.2644 -1.8294 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4194 -1.9457 -3.0927 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6139 -0.3627 -3.4002 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6975 -1.7826 -2.6648 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5993 -0.0509 2.4532 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9779 -0.5481 3.0984 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3088 1.1592 2.6146 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8998 1.1283 0.3692 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9627 -0.4418 -2.2735 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3066 1.2558 -2.0730 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0025 0.8839 -1.7271 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5274 -0.9533 1.4011 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4442 -1.8001 -0.2091 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2033 -1.4200 -1.8732 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5793 -0.8296 -2.2501 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3129 0.4979 1.8941 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0036 0.7380 3.5432 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9107 2.3255 3.4850 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2907 2.1391 2.6115 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9106 -0.9833 -1.8296 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1227 0.4615 -2.6604 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7526 0.5768 -1.8924 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 4 5 2 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 8 10 1 0 10 11 1 0 7 12 1 0 12 13 1 0 2 14 1 0 14 15 1 0 14 16 1 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 2 0 21 23 1 0 23 24 1 0 20 25 1 0 25 26 1 0 9 4 1 0 22 17 1 0 1 27 1 0 1 28 1 0 1 29 1 0 2 30 1 1 3 31 1 0 3 32 1 0 5 33 1 0 6 34 1 0 9 35 1 0 11 36 1 0 11 37 1 0 11 38 1 0 13 39 1 0 13 40 1 0 13 41 1 0 14 42 1 1 15 43 1 0 15 44 1 0 15 45 1 0 16 46 1 0 16 47 1 0 18 48 1 0 19 49 1 0 22 50 1 0 24 51 1 0 24 52 1 0 24 53 1 0 26 54 1 0 26 55 1 0 26 56 1 0 M END

Standard InCHIKey	ORQFDHFZSMXRLM-HZPDHXFCSA-N
Standard InCHI	InChI=1S/C22H30O4/c1-15(11-17-7-9-19(23-3)21(13-17)25-5)16(2)12-18-8-10-20(24-4)22(14-18)26-6/h7-10,13-16H,11-12H2,1-6H3/t15-,16-/m1/s1
SMILES	C[C@H](Cc1ccc(c(c1)OC)OC)[C@H](C)Cc1ccc(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
NPO10994	Sargentodoxa cuneata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10994	Sargentodoxa cuneata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10994	Sargentodoxa cuneata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10994	Sargentodoxa cuneata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10994	Sargentodoxa cuneata	Species	Lardizabalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10994	Sargentodoxa cuneata	Species	Lardizabalaceae	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 NPC162720 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	23336
0.1-0.2	22443
0.2-0.3	3516
0.3-0.4	419
0.4-0.5	102
0.5-0.6	24
0.6-0.7	6
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC165106
0.871	High Similarity	NPC477886
0.7941	Intermediate Similarity	NPC344161
0.7105	Intermediate Similarity	NPC227217
0.7105	Intermediate Similarity	NPC117780
0.6765	Remote Similarity	NPC80241
0.6765	Remote Similarity	NPC301641
0.6765	Remote Similarity	NPC485483
0.6571	Remote Similarity	NPC81067
0.6571	Remote Similarity	NPC602945
0.625	Remote Similarity	NPC292792
0.5882	Remote Similarity	NPC254625
0.5882	Remote Similarity	NPC120075
0.5556	Remote Similarity	NPC274356
0.5556	Remote Similarity	NPC475961
0.5556	Remote Similarity	NPC137685
0.5556	Remote Similarity	NPC101748
0.5532	Remote Similarity	NPC474017
0.5476	Remote Similarity	NPC223807
0.5405	Remote Similarity	NPC303522
0.5405	Remote Similarity	NPC298486
0.5349	Remote Similarity	NPC249788
0.5263	Remote Similarity	NPC165133
0.5263	Remote Similarity	NPC242885
0.5263	Remote Similarity	NPC95614
0.5263	Remote Similarity	NPC76451
0.5263	Remote Similarity	NPC232316
0.5263	Remote Similarity	NPC609746
0.5227	Remote Similarity	NPC482890
0.5227	Remote Similarity	NPC607444
0.5152	Remote Similarity	NPC258425
0.5143	Remote Similarity	NPC474691
0.5128	Remote Similarity	NPC251855
0.5128	Remote Similarity	NPC205502
0.5111	Remote Similarity	NPC485480

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC162720 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3629
0.1-0.2	5023
0.2-0.3	444
0.3-0.4	48
0.4-0.5	5
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	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD5283	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