NPASS Compound

Structure

NPC303189 OpenBabel06302215392D 24 25 0 0 1 0 0 0 0 0999 V2000 -0.8660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3660 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 20 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 17 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 19 1 6 0 0 0 10 9 1 1 0 0 0 10 11 1 0 0 0 0 10 17 1 0 0 0 0 11 12 1 0 0 0 0 11 13 1 0 0 0 0 11 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 1 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 23 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	336.27
Volume:	375.757
LogP:	4.649
LogD:	4.08
LogS:	-5.126
# Rotatable Bonds:	6
TPSA:	46.53
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	2
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.583
Synthetic Accessibility Score:	4.262
Fsp3:	0.857
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.699
MDCK Permeability:	2.5513483706163242e-05
Pgp-inhibitor:	0.965
Pgp-substrate:	0.027
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.014
30% Bioavailability (F30%):	0.125

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.373
Plasma Protein Binding (PPB):	82.34053802490234%
Volume Distribution (VD):	1.124
Pgp-substrate:	15.986083030700684%

ADMET: Metabolism

CYP1A2-inhibitor:	0.101
CYP1A2-substrate:	0.198
CYP2C19-inhibitor:	0.254
CYP2C19-substrate:	0.857
CYP2C9-inhibitor:	0.535
CYP2C9-substrate:	0.264
CYP2D6-inhibitor:	0.008
CYP2D6-substrate:	0.374
CYP3A4-inhibitor:	0.427
CYP3A4-substrate:	0.255

ADMET: Excretion

Clearance (CL):	8.319
Half-life (T1/2):	0.165

ADMET: Toxicity

hERG Blockers:	0.102
Human Hepatotoxicity (H-HT):	0.276
Drug-inuced Liver Injury (DILI):	0.237
AMES Toxicity:	0.004
Rat Oral Acute Toxicity:	0.403
Maximum Recommended Daily Dose:	0.928
Skin Sensitization:	0.66
Carcinogencity:	0.108
Eye Corrosion:	0.715
Eye Irritation:	0.521
Respiratory Toxicity:	0.934

Download Data

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

Natural Product: NPC303189

Natural Product ID:	NPC303189
*Common Name:**	SIICCOSLUNHIQW-JDNANXKCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SIICCOSLUNHIQW-JDNANXKCSA-N
Standard InCHI:	InChI=1S/C21H36O3/c1-14(12-19(23)24-6)8-9-16-15(2)17(22)13-18-20(3,4)10-7-11-21(16,18)5/h14,16-18,22H,2,7-13H2,1,3-6H3/t14-,16+,17-,18+,21-/m1/s1
SMILES:	C[C@H](CC[C@H]1C(=C)[C@@H](C[C@H]2C(C)(C)CCC[C@]12C)O)CC(=O)OC
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

*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
NPO4182	Hygrophorus chrysodon	Species	Hygrophoraceae	Eukaryota	fruiting bodies	n.a.	n.a.	PMID[17253868]
NPO3829	Euphorbia myrsinites	Species	Euphorbiaceae	Eukaryota	n.a.	root	n.a.	PMID[22192329]
NPO623	Amaranthus hypochondriacus	Species	Amaranthaceae	Eukaryota	Flowers	São Paulo, Brazil.		PMID[32156350]
NPO7216	Helicteres angustifolia	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17959	Berberis repens	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7216	Helicteres angustifolia	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7057	Ptarmica ptarmicifolia	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO3423	Teucrium asiaticum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1870	Polyporus dryadeus	Species	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7216	Helicteres angustifolia	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5481	Fomes robiniae	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO275	Amphilophis odorata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO2862	Dendrilla cavernosa	Species	Darwinellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO780	Senecio viscosus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4182	Hygrophorus chrysodon	Species	Hygrophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5143	Millettia ferruginea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17959	Berberis repens	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO623	Amaranthus hypochondriacus	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2302	Sedum litoreum	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11973	Gymnothorax javanicus	Species	Muraenidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1509	Hippeastrum papilio	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7932	Ips confusus	Species	Curculionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25934	Diphasiastrum thyoides	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3829	Euphorbia myrsinites	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26520	Wyethia mollis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6480	Zanthoxylum fraxineum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6081	Limnocharis flava	Species	Alismataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8268	Croton laccifer	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5918	Thermopsis dolichocarpa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4007	Vicia amurensis	Species	Fabaceae	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 NPC303189 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	175
0.1-0.2	1284
0.2-0.3	5161
0.3-0.4	15145
0.4-0.5	8054
0.5-0.6	6473
0.6-0.7	4563
0.7-0.8	1743
0.8-0.85	77
0.85-0.9	18
0.9-0.95	4
0.95-1	0

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 NPC303189 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	173
0.1-0.2	1844
0.2-0.3	3843
0.3-0.4	2198
0.4-0.5	614
0.5-0.6	246
0.6-0.7	199
0.7-0.8	33
0.8-0.85	0
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