NPASS Compound

Structure

NPC80064 OpenBabel06302215322D 31 35 0 0 1 0 0 0 0 0999 V2000 -2.6189 -3.9290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6647 -3.7258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3635 -2.7979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4092 -2.5948 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1080 -1.6668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8462 -1.4637 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.4993 -2.1885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8459 -0.4881 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.6904 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6902 0.9765 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9760 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.0006 1.9760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8462 1.4641 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8465 2.4407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6925 2.9288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5381 2.4402 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -3.3835 2.9283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3838 3.9283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2495 3.4283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2286 2.4397 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -4.2283 1.4631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3829 0.9751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5378 1.4636 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.5376 0.4870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6919 0.9755 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.6916 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8457 -0.4886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.0003 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0948 2.9394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0117 -4.4507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 31 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 8 28 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 11 28 1 0 0 0 0 11 12 1 0 0 0 0 11 13 1 0 0 0 0 13 25 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 23 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 17 20 1 0 0 0 0 20 21 1 0 0 0 0 20 30 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 25 1 0 0 0 0 23 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 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	388.15
Volume:	395.099
LogP:	4.378
LogD:	2.702
LogS:	-3.271
# Rotatable Bonds:	6
TPSA:	127.45
# H-Bond Aceptor:	7
# H-Bond Donor:	5
# Rings:	2
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.229
Synthetic Accessibility Score:	3.474
Fsp3:	0.286
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.025
MDCK Permeability:	2.3406351829180494e-05
Pgp-inhibitor:	0.004
Pgp-substrate:	0.554
Human Intestinal Absorption (HIA):	0.927
20% Bioavailability (F20%):	0.876
30% Bioavailability (F30%):	0.022

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.004
Plasma Protein Binding (PPB):	97.75234985351562%
Volume Distribution (VD):	0.612
Pgp-substrate:	6.849213123321533%

ADMET: Metabolism

CYP1A2-inhibitor:	0.927
CYP1A2-substrate:	0.361
CYP2C19-inhibitor:	0.281
CYP2C19-substrate:	0.058
CYP2C9-inhibitor:	0.768
CYP2C9-substrate:	0.893
CYP2D6-inhibitor:	0.645
CYP2D6-substrate:	0.307
CYP3A4-inhibitor:	0.102
CYP3A4-substrate:	0.149

ADMET: Excretion

Clearance (CL):	6.4
Half-life (T1/2):	0.896

ADMET: Toxicity

hERG Blockers:	0.002
Human Hepatotoxicity (H-HT):	0.092
Drug-inuced Liver Injury (DILI):	0.498
AMES Toxicity:	0.647
Rat Oral Acute Toxicity:	0.153
Maximum Recommended Daily Dose:	0.313
Skin Sensitization:	0.924
Carcinogencity:	0.209
Eye Corrosion:	0.393
Eye Irritation:	0.894
Respiratory Toxicity:	0.124

Download Data

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

Natural Product: NPC80064

Natural Product ID:	NPC80064
*Common Name:**	ONQRKEUAIJMULO-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ONQRKEUAIJMULO-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C30H50O/c1-20(2)9-8-10-21(3)22-13-15-28(7)24-12-11-23-26(4,5)25(31)14-16-29(23)19-30(24,29)18-17-27(22,28)6/h9,21-25,31H,8,10-19H2,1-7H3
SMILES:	CC(=CCCC(C)C1CCC2(C)C3CCC4C(C)(C)C(CCC54CC35CCC12C)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	500213
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002321] Cycloartanols 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
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	n.a.	fruit	n.a.	PMID[12932131]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	fruit	n.a.	PMID[16417304]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	roots	n.a.	n.a.	PMID[16792421]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	branch	n.a.	PMID[17202693]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20460582]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	whole plants	Panshi, Jilin Province, China	2009-JUN	PMID[21534540]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[21534540]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	roots	n.a.	n.a.	PMID[24660966]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	n.a.	fruit	n.a.	PMID[25172746]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25453801]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26702644]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[28383891]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[29148766]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31184480]
NPO26277	Euphorbia hirta	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32141299]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8910532]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	Resin, Exudate, Sap	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Bark	n.a.	n.a.	Database[FooDB]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	Tissue Culture	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	Pericarp	n.a.	n.a.	Database[FooDB]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19048	Pinellia ternata	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26277	Euphorbia hirta	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19048	Pinellia ternata	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26277	Euphorbia hirta	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO19048	Pinellia ternata	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	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]
NPO19048	Pinellia ternata	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16501	Capsicum annuum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26277	Euphorbia hirta	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19048	Pinellia ternata	Species	Araceae	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 NPC80064 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	184
0.1-0.2	1717
0.2-0.3	9128
0.3-0.4	15407
0.4-0.5	5982
0.5-0.6	5395
0.6-0.7	3561
0.7-0.8	1030
0.8-0.85	200
0.85-0.9	58
0.9-0.95	32
0.95-1	3

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 NPC80064 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	188
0.1-0.2	1874
0.2-0.3	4595
0.3-0.4	1760
0.4-0.5	342
0.5-0.6	157
0.6-0.7	178
0.7-0.8	52
0.8-0.85	1
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