NPASS Compound

Structure

NPC143022 OpenBabel06302216192D 29 30 0 0 1 0 0 0 0 0999 V2000 -4.5878 2.5411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0878 1.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0878 1.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5878 2.5411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5878 2.5411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0878 1.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.0878 1.6750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.0878 -0.0570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.6810 -0.9706 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.4242 -1.6397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.2902 -1.1397 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -12.0823 -0.1615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0878 -0.0570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0878 -0.0570 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5878 -0.9230 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 -0.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7601 1.8968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7601 -0.2788 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 2.5691 0.0000 O 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 16 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 15 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 14 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 13 14 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 1 0 0 0 19 21 1 0 0 0 0 21 22 2 0 0 0 0 22 28 1 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 29 1 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 26 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	398.25
Volume:	440.549
LogP:	5.87
LogD:	5.113
LogS:	-4.52
# Rotatable Bonds:	11
TPSA:	66.74
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	2
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.385
Synthetic Accessibility Score:	3.519
Fsp3:	0.44
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:	-4.884
MDCK Permeability:	2.543689879530575e-05
Pgp-inhibitor:	0.781
Pgp-substrate:	0.101
Human Intestinal Absorption (HIA):	0.283
20% Bioavailability (F20%):	0.053
30% Bioavailability (F30%):	0.006

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.027
Plasma Protein Binding (PPB):	96.97074890136719%
Volume Distribution (VD):	2.169
Pgp-substrate:	0.6186778545379639%

ADMET: Metabolism

CYP1A2-inhibitor:	0.603
CYP1A2-substrate:	0.422
CYP2C19-inhibitor:	0.751
CYP2C19-substrate:	0.066
CYP2C9-inhibitor:	0.854
CYP2C9-substrate:	0.972
CYP2D6-inhibitor:	0.845
CYP2D6-substrate:	0.882
CYP3A4-inhibitor:	0.502
CYP3A4-substrate:	0.165

ADMET: Excretion

Clearance (CL):	5.046
Half-life (T1/2):	0.796

ADMET: Toxicity

hERG Blockers:	0.007
Human Hepatotoxicity (H-HT):	0.311
Drug-inuced Liver Injury (DILI):	0.247
AMES Toxicity:	0.002
Rat Oral Acute Toxicity:	0.522
Maximum Recommended Daily Dose:	0.911
Skin Sensitization:	0.717
Carcinogencity:	0.246
Eye Corrosion:	0.005
Eye Irritation:	0.495
Respiratory Toxicity:	0.864

Download Data

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

Natural Product: NPC143022

Natural Product ID:	NPC143022
*Common Name:**	HPVSJNGZYYDDMU-CHVWLSOJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HPVSJNGZYYDDMU-CHVWLSOJSA-N
Standard InCHI:	InChI=1S/C25H34O4/c1-18(8-5-9-19(2)11-7-13-22-14-15-28-17-22)10-6-12-20(3)16-23-24(26)21(4)25(27)29-23/h8,11,14-17,20,26H,5-7,9-10,12-13H2,1-4H3/b18-8+,19-11+,23-16-/t20-/m0/s1
SMILES:	C/C(=CCC/C(=C/CCc1ccoc1)/C)/CCC[C@H](C)/C=C1/C(=C(C)C(=O)O1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	54682873
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]
NPO33253	Irciniidae	Family	Irciniidae	Eukaryota	n.a.	Australian	n.a.	PMID[20346682]
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]
NPO9626	Aconitum finetianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9247	Bupleurum smithii	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
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]
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]

☑ 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
IC50	6
Others	2

Activity Type	# Activity
Cell Line	1
Individual Protein	4
Others	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT178	Individual Protein	Protein-tyrosine phosphatase 1B	Homo sapiens	IC50	=	1500.0	nM	PMID[572213]
NPT1210	Individual Protein	T-cell protein-tyrosine phosphatase	Homo sapiens	IC50	=	800.0	nM	PMID[572213]
NPT287	Individual Protein	Leukocyte common antigen	Homo sapiens	IC50	=	1200.0	nM	PMID[572213]
NPT1211	Individual Protein	Dual specificity protein phosphatase 3	Homo sapiens	IC50	=	6000.0	nM	PMID[572213]
NPT1229	Cell Line	Huh-7	Homo sapiens	IC50	>	50000.0	nM	PMID[572213]
NPT2	Others	Unspecified		IC50	>	50000.0	nM	PMID[572213]
NPT2	Others	Unspecified		Ratio IC50	=	2.0	n.a.	PMID[572213]
NPT2	Others	Unspecified		Ratio IC50	=	4.0	n.a.	PMID[572213]

☑ 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 NPC143022 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 NPC143022 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