NPASS Compound

Structure

NPC490298 OpenBabel06302216222D 40 43 0 0 1 0 0 0 0 0999 V2000 -0.2257 -2.6361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1810 -1.7226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4067 -0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4013 -1.0181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9890 -0.2091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9836 -0.3136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3903 -1.2271 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.8903 -2.0932 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5594 -2.8363 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4730 -2.4296 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -4.3684 -1.4350 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -5.1116 -0.7659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0627 -1.0749 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3390 -2.9296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3390 -3.9296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2050 -4.4296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0711 -3.9296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9371 -4.4296 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.9371 -5.4296 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -7.0711 -5.9296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0711 -6.9296 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.8031 -5.9296 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -8.8031 -6.9296 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.6691 -5.4296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.6691 -4.4296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.5352 -3.9296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.4012 -4.4296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.2672 -3.9296 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.4012 -5.4296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.2672 -5.9296 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.2672 -6.9296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.5352 -5.9296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0711 -2.9296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9371 -2.4296 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.8031 -2.9296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2050 -2.4296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5823 0.7045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9945 0.1045 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 39 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 37 2 0 0 0 0 6 7 1 0 0 0 0 7 11 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 14 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 14 36 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 17 33 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 22 1 0 0 0 0 20 21 1 0 0 0 0 22 23 1 0 0 0 0 22 24 1 0 0 0 0 24 32 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 27 28 1 0 0 0 0 27 29 1 0 0 0 0 29 30 1 0 0 0 0 29 32 2 0 0 0 0 30 31 1 0 0 0 0 33 34 1 0 0 0 0 33 36 2 0 0 0 0 34 35 1 0 0 0 0 37 38 1 0 0 0 0 38 39 2 0 0 0 0 39 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	556.23
Volume:	557.384
LogP:	1.869
LogD:	2.496
LogS:	-4.231
# Rotatable Bonds:	12
TPSA:	147.3
# H-Bond Aceptor:	10
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.225
Synthetic Accessibility Score:	4.127
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.576
MDCK Permeability:	1.2366926966933534e-05
Pgp-inhibitor:	0.018
Pgp-substrate:	0.095
Human Intestinal Absorption (HIA):	0.533
20% Bioavailability (F20%):	0.016
30% Bioavailability (F30%):	0.016

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.16
Plasma Protein Binding (PPB):	91.88909912109375%
Volume Distribution (VD):	0.646
Pgp-substrate:	7.605267524719238%

ADMET: Metabolism

CYP1A2-inhibitor:	0.015
CYP1A2-substrate:	0.807
CYP2C19-inhibitor:	0.041
CYP2C19-substrate:	0.828
CYP2C9-inhibitor:	0.151
CYP2C9-substrate:	0.769
CYP2D6-inhibitor:	0.196
CYP2D6-substrate:	0.912
CYP3A4-inhibitor:	0.713
CYP3A4-substrate:	0.889

ADMET: Excretion

Clearance (CL):	11.944
Half-life (T1/2):	0.751

ADMET: Toxicity

hERG Blockers:	0.153
Human Hepatotoxicity (H-HT):	0.153
Drug-inuced Liver Injury (DILI):	0.158
AMES Toxicity:	0.098
Rat Oral Acute Toxicity:	0.16
Maximum Recommended Daily Dose:	0.1
Skin Sensitization:	0.21
Carcinogencity:	0.07
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.014

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC490298

Natural Product ID:	NPC490298
*Common Name:**	Lariciresinol-sesquilignan
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MWGNJVCCJCKLGJ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C30H36O10/c1-36-25-11-17(4-7-22(25)33)10-20-16-39-30(21(20)14-31)19-6-9-24(27(13-19)38-3)40-28(15-32)29(35)18-5-8-23(34)26(12-18)37-2/h4-9,11-13,20-21,28-35H,10,14-16H2,1-3H3
SMILES:	COC1=CC(CC2COC(C2CO)C2=CC=C(OC(CO)C(O)C3=CC=C(O)C(OC)=C3)C(OC)=C2)=CC=C1O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans [CHEMONTID:0001604] Tetrahydrofuran lignans [CHEMONTID:0003422] 7,9'-epoxylignans

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	DOI[10.1016/S0963-9969(99)00095-2]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Leaves (mother plant)	Suwon, Korea	2011-Sep	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Roots (runner plant)	Suwon, Korea	2011-Sep	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruits	Suwon, Korea	2012-Nov	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Leaves	Suwon, Korea		DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Runners	Suwon, Korea	2011-Sep	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Leaves (runner plant)	Suwon, Korea	2011-Sep	DOI[10.7235/HORT.2013.12200]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Roots (mother plant)	Suwon, Korea	2011-Sep	DOI[10.7235/HORT.2013.12200]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	seed	n.a.	PMID[11540412]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1453178]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[15568772]
NPO7156	Vaccinium myrtillus	Species	Ericaceae	Eukaryota	n.a.	fruit	n.a.	PMID[16417304]
NPO7156	Vaccinium myrtillus	Species	Ericaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO7156	Vaccinium myrtillus	Species	Ericaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7156	Vaccinium myrtillus	Species	Ericaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO7156	Vaccinium myrtillus	Species	Ericaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO7156	Vaccinium myrtillus	Species	Ericaceae	Eukaryota	Fruit Juice	n.a.	n.a.	Database[FooDB]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO7156	Vaccinium myrtillus	Species	Ericaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO7156	Vaccinium myrtillus	Species	Ericaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO7156	Vaccinium myrtillus	Species	Ericaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO10339	Fragaria x ananassa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7156	Vaccinium myrtillus	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10339	Fragaria x ananassa	Species	Rosaceae	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	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
NPO24778	NPC490298	Dried Or Powder	n.a.	0.082999997	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO10339	NPC490298	n.a.	Fruits	0.1	n.a.	n.a.	mg/100g of FW	Database [Phenol-Explorer]
NPO7156	NPC490298	n.a.	Fruits	0.09	n.a.	n.a.	mg/100g of FW	Database [Phenol-Explorer]

☑ 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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC490298 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score	Similarity Level	Natural Product ID

Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC490298 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score	Similarity Level	Drug ID	Developmental Stage

Bioactivity similarity: Similar Natural Products in NPASS

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