NPASS Compound

Structure

NPC260196 OpenBabel06302216222D 27 28 0 0 1 0 0 0 0 0999 V2000 6.9282 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -4.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 C 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 4.3301 -2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 O 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 1.7321 -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 -0.8660 -1.5000 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 -2.5981 -1.5000 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 -2.5981 0.5000 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 0.0000 0.0000 0.0000 C 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 4 2 0 0 0 0 3 5 1 0 0 0 0 5 13 1 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 9 1 1 0 0 0 8 10 1 0 0 0 0 10 11 2 0 0 0 0 10 13 1 0 0 0 0 11 12 1 0 0 0 0 13 14 1 6 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 27 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 24 2 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 26 27 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	378.13
Volume:	371.934
LogP:	1.548
LogD:	1.56
LogS:	-2.077
# Rotatable Bonds:	8
TPSA:	122.52
# H-Bond Aceptor:	8
# H-Bond Donor:	3
# Rings:	2
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.387
Synthetic Accessibility Score:	3.835
Fsp3:	0.368
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.051
MDCK Permeability:	4.648364847525954e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.091
Human Intestinal Absorption (HIA):	0.294
20% Bioavailability (F20%):	0.906
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.1
Plasma Protein Binding (PPB):	80.61066436767578%
Volume Distribution (VD):	0.948
Pgp-substrate:	17.839073181152344%

ADMET: Metabolism

CYP1A2-inhibitor:	0.765
CYP1A2-substrate:	0.168
CYP2C19-inhibitor:	0.82
CYP2C19-substrate:	0.067
CYP2C9-inhibitor:	0.852
CYP2C9-substrate:	0.776
CYP2D6-inhibitor:	0.837
CYP2D6-substrate:	0.223
CYP3A4-inhibitor:	0.75
CYP3A4-substrate:	0.263

ADMET: Excretion

Clearance (CL):	10.958
Half-life (T1/2):	0.899

ADMET: Toxicity

hERG Blockers:	0.031
Human Hepatotoxicity (H-HT):	0.604
Drug-inuced Liver Injury (DILI):	0.919
AMES Toxicity:	0.895
Rat Oral Acute Toxicity:	0.846
Maximum Recommended Daily Dose:	0.983
Skin Sensitization:	0.641
Carcinogencity:	0.856
Eye Corrosion:	0.04
Eye Irritation:	0.794
Respiratory Toxicity:	0.933

Download Data

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

Natural Product: NPC260196

Natural Product ID:	NPC260196
*Common Name:**	Oleuropein-aglycone
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BIWKXNFEOZXNLX-BBHIFXBUSA-N
Standard InCHI:	InChI=1S/C19H22O8/c1-3-12-13(14(18(23)25-2)10-27-19(12)24)9-17(22)26-7-6-11-4-5-15(20)16(21)8-11/h3-5,8,10,13,19-21,24H,6-7,9H2,1-2H3/b12-3+/t13-,19+/m0/s1
SMILES:	C/C=C/1[C@H](CC(=O)OCCc2ccc(c(c2)O)O)C(=CO[C@H]1O)C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001549] Monoterpenoids [CHEMONTID:0001565] Iridoids and derivatives

*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
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[12802735]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[18384095]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22014120]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[22014120]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22014168]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23540838]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24295708]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	leaf	n.a.	PMID[25102361]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[25306330]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	Oil	n.a.	n.a.	Database[FooDB]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28608	Olea europaea	Species	Oleaceae	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
NPO28608	NPC260196	Oil	n.a.	12.0617789	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO28608	NPC260196	Oil	n.a.	3.669524876	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO28608	NPC260196	Oil	n.a.	12.54530335	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO28608	NPC260196	Raw	n.a.	58.5	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO28608	NPC260196	Raw	n.a.	81.82414375	n.a.	n.a.	mg/100g	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

Activity Type	# Activity
IC50	1
Others	2

Activity Type	# Activity
Individual Protein	1
Others	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT51	Individual Protein	Microtubule-associated protein tau	Homo sapiens	Inhibition	=	79.0	%	PMID[452419]
NPT2	Others	Unspecified		IC50	=	1300.0	nM	PMID[452419]
NPT2	Others	Unspecified		Inhibition	=	84.0	%	PMID[452419]

☑ 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 NPC260196 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	276
0.1-0.2	1191
0.2-0.3	3300
0.3-0.4	8172
0.4-0.5	10685
0.5-0.6	5013
0.6-0.7	10838
0.7-0.8	3057
0.8-0.85	158
0.85-0.9	5
0.9-0.95	1
0.95-1	1

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 NPC260196 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	238
0.1-0.2	793
0.2-0.3	1718
0.3-0.4	2812
0.4-0.5	1865
0.5-0.6	1196
0.6-0.7	481
0.7-0.8	46
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
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