NPASS Compound

Structure

NPC112804 OpenBabel06302215112D 27 27 0 0 0 0 0 0 0 0999 V2000 14.0652 4.7224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.4774 3.9133 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.4829 4.0179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.0762 4.9314 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.0816 5.0359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.4938 4.2269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4993 4.3315 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9115 3.5224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9170 3.6270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3292 2.8180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3347 2.9225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7469 2.1135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7524 2.2180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1646 1.4090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1701 1.5135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5823 0.7045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3090 -0.9511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -1.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -2.5388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 -0.9511 0.0000 O 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 4.5714 0.4954 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7360 1.9044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.9006 3.3134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8841 2.9998 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 27 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 2 0 0 0 0 6 26 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 2 0 0 0 0 10 25 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 24 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 23 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	370.29
Volume:	434.161
LogP:	7.655
LogD:	5.969
LogS:	-4.583
# Rotatable Bonds:	12
TPSA:	33.37
# H-Bond Aceptor:	2
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.377
Synthetic Accessibility Score:	3.34
Fsp3:	0.52
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:	-4.888
MDCK Permeability:	2.410847446299158e-05
Pgp-inhibitor:	0.073
Pgp-substrate:	0.049
Human Intestinal Absorption (HIA):	0.481
20% Bioavailability (F20%):	0.807
30% Bioavailability (F30%):	0.931

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.078
Plasma Protein Binding (PPB):	95.85604095458984%
Volume Distribution (VD):	2.32
Pgp-substrate:	0.9194884300231934%

ADMET: Metabolism

CYP1A2-inhibitor:	0.409
CYP1A2-substrate:	0.181
CYP2C19-inhibitor:	0.445
CYP2C19-substrate:	0.056
CYP2C9-inhibitor:	0.619
CYP2C9-substrate:	0.983
CYP2D6-inhibitor:	0.76
CYP2D6-substrate:	0.629
CYP3A4-inhibitor:	0.449
CYP3A4-substrate:	0.114

ADMET: Excretion

Clearance (CL):	5.788
Half-life (T1/2):	0.367

ADMET: Toxicity

hERG Blockers:	0.012
Human Hepatotoxicity (H-HT):	0.44
Drug-inuced Liver Injury (DILI):	0.006
AMES Toxicity:	0.0
Rat Oral Acute Toxicity:	0.002
Maximum Recommended Daily Dose:	0.679
Skin Sensitization:	0.958
Carcinogencity:	0.026
Eye Corrosion:	0.104
Eye Irritation:	0.765
Respiratory Toxicity:	0.015

Download Data

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

Natural Product: NPC112804

Natural Product ID:	NPC112804
*Common Name:**	NSOLOFCWLXZPAF-MLAGYPMBSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NSOLOFCWLXZPAF-MLAGYPMBSA-N
Standard InCHI:	InChI=1S/C25H38O2/c1-20(2)10-6-11-21(3)12-7-13-22(4)14-8-15-23(5)16-9-17-24-18-25(26)27-19-24/h10,12,14,16,18H,6-9,11,13,15,17,19H2,1-5H3/b21-12+,22-14+,23-16+
SMILES:	CC(=CCC/C(=C/CC/C(=C/CC/C(=C/CCC1=CC(=O)OC1)/C)/C)/C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10090584
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001538] Diterpene lactones

*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
NPO8737	Saussurea muliensis	Species	Asteraceae	Eukaryota	flowers and roots	Muli Autonomous County of Sichuan, China	2005-AUG	PMID[18419156]
NPO9247	Bupleurum smithii	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9626	Aconitum finetianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3770	Drosera rotundifolia	Species	Droseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9626	Aconitum finetianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9247	Bupleurum smithii	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3770	Drosera rotundifolia	Species	Droseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11920	Geraea canescens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9247	Bupleurum smithii	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9626	Aconitum finetianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3770	Drosera rotundifolia	Species	Droseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8737	Saussurea muliensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9247	Bupleurum smithii	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11920	Geraea canescens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9626	Aconitum finetianum	Species	Ranunculaceae	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

Activity Type	# Activity
Others	4

Activity Type	# Activity
Organism	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Supression	=	65.0	%	PMID[466552]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Histamine release	=	4.0	%	PMID[466552]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Histamine release	=	11.0	%	PMID[466552]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Histamine release	=	30.0	%	PMID[466552]

☑ 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 NPC112804 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 NPC112804 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