NPASS Compound

Structure

NPC279017 OpenBabel06302216002D 24 25 0 0 0 0 0 0 0 0999 V2000 1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 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 -0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 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 17 2 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 4 14 2 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 13 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 14 15 1 0 0 0 0 14 24 1 0 0 0 0 15 16 2 0 0 0 0 15 22 1 0 0 0 0 16 17 1 0 0 0 0 16 20 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 20 21 1 0 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	330.15
Volume:	345.563
LogP:	3.31
LogD:	3.352
LogS:	-4.034
# Rotatable Bonds:	7
TPSA:	57.15
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.839
Synthetic Accessibility Score:	2.475
Fsp3:	0.263
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.605
MDCK Permeability:	1.3980711628391873e-05
Pgp-inhibitor:	0.975
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.001
30% Bioavailability (F30%):	0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.062
Plasma Protein Binding (PPB):	96.63018798828125%
Volume Distribution (VD):	0.356
Pgp-substrate:	4.770394325256348%

ADMET: Metabolism

CYP1A2-inhibitor:	0.834
CYP1A2-substrate:	0.953
CYP2C19-inhibitor:	0.93
CYP2C19-substrate:	0.89
CYP2C9-inhibitor:	0.7
CYP2C9-substrate:	0.921
CYP2D6-inhibitor:	0.477
CYP2D6-substrate:	0.874
CYP3A4-inhibitor:	0.797
CYP3A4-substrate:	0.868

ADMET: Excretion

Clearance (CL):	5.51
Half-life (T1/2):	0.591

ADMET: Toxicity

hERG Blockers:	0.264
Human Hepatotoxicity (H-HT):	0.06
Drug-inuced Liver Injury (DILI):	0.532
AMES Toxicity:	0.038
Rat Oral Acute Toxicity:	0.354
Maximum Recommended Daily Dose:	0.037
Skin Sensitization:	0.927
Carcinogencity:	0.145
Eye Corrosion:	0.004
Eye Irritation:	0.871
Respiratory Toxicity:	0.029

Download Data

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

Natural Product: NPC279017

Natural Product ID:	NPC279017
*Common Name:**	IHWNGWBUZVFFLB-XYOKQWHBSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IHWNGWBUZVFFLB-XYOKQWHBSA-N
Standard InCHI:	InChI=1S/C19H22O5/c1-21-16-14(12-8-11-13-9-6-5-7-10-13)15(20)17(22-2)19(24-4)18(16)23-3/h5-10,12,20H,11H2,1-4H3/b12-8+
SMILES:	COc1c(/C=C/Cc2ccccc2)c(c(c(c1OC)OC)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	100953061
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0003467] Linear 1,3-diarylpropanoids [CHEMONTID:0003496] Cinnamylphenols

*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
NPO9585	Oenothera biennis	Species	Onagraceae	Eukaryota	Seeds	Yichun, Heilongjiang Province, China	2018-Sep	PMID[31292343]
NPO9585	Oenothera biennis	Species	Onagraceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO9585	Oenothera biennis	Species	Onagraceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO9585	Oenothera biennis	Species	Onagraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5309	Eucalyptus jensenii	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3526	Moronobea pulchra	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2007	Hygrophorus persoonii	Species	Hygrophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25029	Trifolium incarnatum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1670	Salvia beckeri	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1285	Helenium linifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7411	Pandanus odoratissimus	Species	Pandanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7022	0tholaena neglecta	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8784	Podocytisus caramanicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13622	Lespedeza thunbergii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8929	Adenium boehmianum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO141	Scutellaria alpina	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9859	Argyrolobium uniflorum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26168	Isatis quadrialata	Species	Brassicaceae	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

☑ 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 NPC279017 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	413
0.1-0.2	1811
0.2-0.3	6079
0.3-0.4	13117
0.4-0.5	3886
0.5-0.6	4438
0.6-0.7	7206
0.7-0.8	4390
0.8-0.85	731
0.85-0.9	377
0.9-0.95	209
0.95-1	40

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 NPC279017 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	364
0.1-0.2	954
0.2-0.3	1937
0.3-0.4	2805
0.4-0.5	1558
0.5-0.6	888
0.6-0.7	532
0.7-0.8	101
0.8-0.85	8
0.85-0.9	2
0.9-0.95	1
0.95-1	0

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