NPASS Compound

Structure

NPC70388 OpenBabel06302215342D 31 35 0 0 1 0 0 0 0 0999 V2000 -1.0936 -0.4530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8420 0.4861 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6133 1.0780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8420 1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.9444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8420 1.4583 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.8420 2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6839 1.9444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5259 1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5259 0.4861 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 4.2098 1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6839 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6839 -0.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5259 -1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3679 -0.9722 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 4.2098 -1.4583 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.3679 -1.9444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2098 -2.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0518 -2.9167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8938 -2.4306 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 5.8938 -1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8660 -1.4583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3799 -0.6164 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0518 -0.9722 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 5.0518 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2098 0.4861 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3679 0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.3679 0.9722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7358 -2.9167 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8420 0.4861 0.0000 C 0 0 3 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 31 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 30 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 27 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 12 13 2 0 0 0 0 12 30 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 27 1 0 0 0 0 15 16 1 0 0 0 0 16 24 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 29 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 21 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 30 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	426.39
Volume:	490.807
LogP:	7.815
LogD:	5.742
LogS:	-6.142
# Rotatable Bonds:	0
TPSA:	20.23
# H-Bond Aceptor:	1
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.387
Synthetic Accessibility Score:	4.56
Fsp3:	0.933
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.034
MDCK Permeability:	6.761615622963291e-06
Pgp-inhibitor:	0.049
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.03
20% Bioavailability (F20%):	0.257
30% Bioavailability (F30%):	0.877

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.749
Plasma Protein Binding (PPB):	99.78449249267578%
Volume Distribution (VD):	1.82
Pgp-substrate:	2.519968271255493%

ADMET: Metabolism

CYP1A2-inhibitor:	0.021
CYP1A2-substrate:	0.402
CYP2C19-inhibitor:	0.061
CYP2C19-substrate:	0.968
CYP2C9-inhibitor:	0.093
CYP2C9-substrate:	0.488
CYP2D6-inhibitor:	0.114
CYP2D6-substrate:	0.748
CYP3A4-inhibitor:	0.2
CYP3A4-substrate:	0.522

ADMET: Excretion

Clearance (CL):	15.308
Half-life (T1/2):	0.009

ADMET: Toxicity

hERG Blockers:	0.004
Human Hepatotoxicity (H-HT):	0.156
Drug-inuced Liver Injury (DILI):	0.008
AMES Toxicity:	0.018
Rat Oral Acute Toxicity:	0.095
Maximum Recommended Daily Dose:	0.715
Skin Sensitization:	0.035
Carcinogencity:	0.017
Eye Corrosion:	0.003
Eye Irritation:	0.413
Respiratory Toxicity:	0.965

Download Data

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

Natural Product: NPC70388

Natural Product ID:	NPC70388
*Common Name:**	JFSHUTJDVKUMTJ-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JFSHUTJDVKUMTJ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C30H50O/c1-25(2)15-16-27(5)17-18-29(7)20(21(27)19-25)9-10-23-28(6)13-12-24(31)26(3,4)22(28)11-14-30(23,29)8/h9,21-24,31H,10-19H2,1-8H3
SMILES:	CC1(C)CCC2(C)CCC3(C)C(=CCC4C5(C)CCC(C(C)(C)C5CCC34C)O)C2C1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	225689
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1007/s11418-006-0112-9]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	stem	n.a.	DOI[10.1007/s11418-006-0112-9]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	flower	n.a.	DOI[10.1007/s11418-006-0112-9]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11816-015-0350-y]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/0031-9422(86)88033-5]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	stem	n.a.	DOI[10.1016/0031-9422(86)88033-5]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	whole plant	n.a.	n.a.	DOI[10.1016/j.tetlet.2016.12.029]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[17520525]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19919095]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22966846]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	flower buds and leaves	Khon Kaen province, Thailand	2010	PMID[23270663]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[23642481]
NPO15315	Boswellia carterii	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24195447]
NPO15315	Boswellia carterii	Species	Burseraceae	Eukaryota	Gum resin	n.a.	n.a.	PMID[26457560]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Flowers	n.a.	n.a.	PMID[26462418]
NPO26277	Euphorbia hirta	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32141299]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6387056]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Rhizome	n.a.	n.a.	Database[FooDB]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO10506	Artemisia apiacea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26785	Taraxacum mongolicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15315	Boswellia carterii	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26277	Euphorbia hirta	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11697	Cirsium setosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26785	Taraxacum mongolicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10506	Artemisia apiacea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11697	Cirsium setosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15315	Boswellia carterii	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26277	Euphorbia hirta	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10506	Artemisia apiacea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26785	Taraxacum mongolicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15315	Boswellia carterii	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23706	Breea segeta	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26785	Taraxacum mongolicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13668	Taraxacum platycarpum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10506	Artemisia apiacea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11697	Cirsium setosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO23327	Taraxacum coreanum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1596	Taraxacum borealisinense	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15315	Boswellia carterii	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26277	Euphorbia hirta	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11697	Cirsium setosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13668	Taraxacum platycarpum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15315	Boswellia carterii	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17494	Prunella vulgaris	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10506	Artemisia apiacea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26785	Taraxacum mongolicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26622	Taraxacum officinale	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23327	Taraxacum coreanum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26277	Euphorbia hirta	Species	Euphorbiaceae	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 NPC70388 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	212
0.1-0.2	1933
0.2-0.3	8365
0.3-0.4	16371
0.4-0.5	6344
0.5-0.6	4788
0.6-0.7	3337
0.7-0.8	969
0.8-0.85	237
0.85-0.9	101
0.9-0.95	13
0.95-1	27

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 NPC70388 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	224
0.1-0.2	2164
0.2-0.3	4232
0.3-0.4	1825
0.4-0.5	356
0.5-0.6	192
0.6-0.7	141
0.7-0.8	13
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	1

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