NPASS Compound

Structure

NPC297292 OpenBabel06302215212D 25 28 0 0 1 0 0 0 0 0999 V2000 -2.7136 3.0772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1957 2.4280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5586 1.6737 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1953 0.9197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3792 0.7335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7249 1.2556 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 0.8371 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4315 0.0106 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4315 -0.8158 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7249 1.2556 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7249 2.0926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.5112 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7249 2.0926 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3796 2.6144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1950 3.4242 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5707 1.5718 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4775 1.1637 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.3376 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4498 0.8371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2763 0.8371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8631 1.5528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4498 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7249 -0.4185 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7157 -0.4132 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 14 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 1 0 0 0 3 16 1 0 0 0 0 4 5 1 0 0 0 0 6 5 1 6 0 0 0 6 7 1 0 0 0 0 6 13 1 0 0 0 0 7 24 1 0 0 0 0 7 8 1 6 0 0 0 7 10 1 0 0 0 0 8 9 1 0 0 0 0 10 11 1 6 0 0 0 10 19 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 18 1 6 0 0 0 13 14 1 1 0 0 0 13 16 1 0 0 0 0 14 15 2 0 0 0 0 16 17 1 6 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 19 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	350.21
Volume:	358.929
LogP:	1.017
LogD:	0.273
LogS:	-3.293
# Rotatable Bonds:	1
TPSA:	97.99
# H-Bond Aceptor:	5
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.53
Synthetic Accessibility Score:	6.138
Fsp3:	0.85
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.026
MDCK Permeability:	7.59491149437963e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.044
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.037
30% Bioavailability (F30%):	0.167

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.399
Plasma Protein Binding (PPB):	47.92672348022461%
Volume Distribution (VD):	0.715
Pgp-substrate:	56.79225158691406%

ADMET: Metabolism

CYP1A2-inhibitor:	0.014
CYP1A2-substrate:	0.067
CYP2C19-inhibitor:	0.007
CYP2C19-substrate:	0.554
CYP2C9-inhibitor:	0.015
CYP2C9-substrate:	0.231
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.316
CYP3A4-inhibitor:	0.009
CYP3A4-substrate:	0.161

ADMET: Excretion

Clearance (CL):	2.811
Half-life (T1/2):	0.586

ADMET: Toxicity

hERG Blockers:	0.193
Human Hepatotoxicity (H-HT):	0.105
Drug-inuced Liver Injury (DILI):	0.057
AMES Toxicity:	0.462
Rat Oral Acute Toxicity:	0.963
Maximum Recommended Daily Dose:	0.984
Skin Sensitization:	0.683
Carcinogencity:	0.02
Eye Corrosion:	0.008
Eye Irritation:	0.127
Respiratory Toxicity:	0.972

Download Data

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

Natural Product: NPC297292

Natural Product ID:	NPC297292
*Common Name:**	WHSUEVLJUHPROF-IMZDMEOWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WHSUEVLJUHPROF-IMZDMEOWSA-N
Standard InCHI:	InChI=1S/C20H30O5/c1-10-11-4-5-12-19(9-21)13(18(2,3)7-6-14(19)22)8-15(23)20(12,16(10)24)17(11)25/h11-15,17,21-23,25H,1,4-9H2,2-3H3/t11-,12-,13+,14+,15+,17+,19-,20-/m0/s1
SMILES:	C=C1[C@@H]2CC[C@H]3[C@@]4(CO)[C@H](C[C@H]([C@@]3(C1=O)[C@@H]2O)O)C(C)(C)CC[C@H]4O
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:0001551] Diterpenoids [CHEMONTID:0003782] Kaurane diterpenoids

*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
NPO8282	Physalis viscosa	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15730264]
NPO1680	Physalis angulata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17580910]
NPO6895	Elateriospermum tapos	Species	Euphorbiaceae	Eukaryota	leaves and stem	Nakorn Si Thammarat Province, Thailand	2004-MAR	PMID[18179177]
NPO1680	Physalis angulata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21954931]
NPO1680	Physalis angulata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23270478]
NPO1680	Physalis angulata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25396337]
NPO1680	Physalis angulata	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27295506]
NPO26123	Isodon serra	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32993289]
NPO458	Ophiarachna incrassata	Species	Ophiodermatidae	Eukaryota	n.a.	n.a.	n.a.	PMID[7853009]
NPO74	Artemisia indica	Species	Asteraceae	Eukaryota	n.a.	stem	n.a.	PMID[9748386]
NPO4014	Erigeron breviscapus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2248	Aiphanes horrida	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26123	Isodon serra	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4014	Erigeron breviscapus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4014	Erigeron breviscapus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO74	Artemisia indica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19924	Trachycladiella aurea	Species	Meteoriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26123	Isodon serra	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3591	Halleria lucida	Species	Stilbaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4530	Erysimum marschallianum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4989	Tricholoma orirubens	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO458	Ophiarachna incrassata	Species	Ophiodermatidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4014	Erigeron breviscapus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6318	Caulerpa flexilis	Species	Caulerpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10263	Alternaria tagetica	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1361	Chenopodium vulvaria	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14622	Micromonospora lacustris	Species	Micromonosporaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO6895	Elateriospermum tapos	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2313	Jungia spectabilis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8282	Physalis viscosa	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27832	Pyrobaculum neutrophilum	Species	Thermoproteaceae	Archaea	n.a.	n.a.	n.a.	Database[UNPD]
NPO2248	Aiphanes horrida	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1680	Physalis angulata	Species	Solanaceae	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 NPC297292 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	1694
0.2-0.3	5971
0.3-0.4	11434
0.4-0.5	10035
0.5-0.6	5962
0.6-0.7	5239
0.7-0.8	1832
0.8-0.85	167
0.85-0.9	70
0.9-0.95	50
0.95-1	31

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 NPC297292 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	194
0.1-0.2	2089
0.2-0.3	4128
0.3-0.4	1820
0.4-0.5	482
0.5-0.6	164
0.6-0.7	155
0.7-0.8	117
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