NPASS Compound

Structure

NPC148104 OpenBabel06302216192D 26 28 0 0 1 0 0 0 0 0999 V2000 -0.1896 -1.6828 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6235 -0.7818 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6235 -0.7818 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2470 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0245 0.9749 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8829 1.4878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9725 2.4838 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6360 0.8299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6109 1.0524 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2430 -0.0896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1235 1.4088 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2225 0.9749 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2105 1.1294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6359 1.4878 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.3890 0.8299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9960 -0.0896 0.0000 C 0 0 1 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 1.5089 -0.9481 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5088 -0.9331 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9958 -0.0597 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0217 -1.7916 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7256 2.4838 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6329 2.9042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7226 3.9001 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4506 2.3285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1235 2.4088 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 17 1 0 0 0 0 4 3 1 6 0 0 0 4 5 1 0 0 0 0 4 10 1 0 0 0 0 5 6 1 1 0 0 0 5 11 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 11 12 1 0 0 0 0 11 26 1 1 0 0 0 12 17 1 0 0 0 0 12 13 1 1 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 14 22 1 6 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 6 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	103.98
Volume:	86.27
LogP:	1.883
LogD:	2.26
LogS:	-0.849
# Rotatable Bonds:	0
TPSA:	0.0
# H-Bond Aceptor:	0
# H-Bond Donor:	0
# Rings:	1
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.46
Synthetic Accessibility Score:	5.198
Fsp3:	0.333
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.977
MDCK Permeability:	4.0376235119765624e-06
Pgp-inhibitor:	0.002
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.001
30% Bioavailability (F30%):	0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.948
Plasma Protein Binding (PPB):	66.31604766845703%
Volume Distribution (VD):	1.034
Pgp-substrate:	23.831865310668945%

ADMET: Metabolism

CYP1A2-inhibitor:	0.981
CYP1A2-substrate:	0.331
CYP2C19-inhibitor:	0.203
CYP2C19-substrate:	0.515
CYP2C9-inhibitor:	0.068
CYP2C9-substrate:	0.854
CYP2D6-inhibitor:	0.541
CYP2D6-substrate:	0.877
CYP3A4-inhibitor:	0.104
CYP3A4-substrate:	0.203

ADMET: Excretion

Clearance (CL):	10.749
Half-life (T1/2):	0.878

ADMET: Toxicity

hERG Blockers:	0.007
Human Hepatotoxicity (H-HT):	0.084
Drug-inuced Liver Injury (DILI):	0.966
AMES Toxicity:	0.519
Rat Oral Acute Toxicity:	0.935
Maximum Recommended Daily Dose:	0.041
Skin Sensitization:	0.951
Carcinogencity:	0.067
Eye Corrosion:	0.977
Eye Irritation:	0.996
Respiratory Toxicity:	0.951

Download Data

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

Natural Product: NPC148104

Natural Product ID:	NPC148104
*Common Name:**	QFJNAUKGMNMIGV-HTFPEHADSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QFJNAUKGMNMIGV-HTFPEHADSA-N
Standard InCHI:	InChI=1S/C19H26O7/c1-8-6-12-15(9(2)18(23)26-12)17(22)19(5)14(25-11(4)21)7-13(16(8)19)24-10(3)20/h8,12-17,22H,2,6-7H2,1,3-5H3/t8-,12+,13+,14-,15-,16-,17-,19-/m1/s1
SMILES:	C[C@@H]1C[C@H]2[C@@H](C(=C)C(=O)O2)[C@H]([C@]2(C)[C@@H](C[C@@H]([C@@H]12)OC(=O)C)OC(=O)C)O
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:0001283] Terpene lactones [CHEMONTID:0001543] Sesquiterpene 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
NPO17767	Artocarpus heterophyllus	Species	Moraceae	Eukaryota	n.a.	root	n.a.	DOI[10.1016/0031-9422(95)00135-T]
NPO17312	Croomia heterosepala	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21902195]
NPO17767	Artocarpus heterophyllus	Species	Moraceae	Eukaryota	Wood	n.a.	n.a.	PMID[23113717]
NPO17767	Artocarpus heterophyllus	Species	Moraceae	Eukaryota	n.a.	formosan	n.a.	PMID[8864236]
NPO17767	Artocarpus heterophyllus	Species	Moraceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO17767	Artocarpus heterophyllus	Species	Moraceae	Eukaryota	Latex Exudate	n.a.	n.a.	Database[FooDB]
NPO17767	Artocarpus heterophyllus	Species	Moraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO17767	Artocarpus heterophyllus	Species	Moraceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO17767	Artocarpus heterophyllus	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25921	Papaver nudicaule	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25921	Papaver nudicaule	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17767	Artocarpus heterophyllus	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2282	Ageratina altissima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25921	Papaver nudicaule	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16931	Cichorium glandulosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5073	Fontainea picrosperma	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25921	Papaver nudicaule	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2282	Ageratina altissima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18092	Cleyera japonica	Species	Pentaphylacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12643	Delphinium dyctiocarpum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16931	Cichorium glandulosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17529	Horsfieldia irya	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6713	Eria confusa	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14825	Artemisia oliveriana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17767	Artocarpus heterophyllus	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17312	Croomia heterosepala	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6487	Peltophorum africanum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28437	Hypomyces aurantius	Species	Hypocreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16576	Hopea chinensis	Species	Dipterocarpaceae	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 NPC148104 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	250
0.1-0.2	1790
0.2-0.3	6417
0.3-0.4	15254
0.4-0.5	8203
0.5-0.6	7313
0.6-0.7	2887
0.7-0.8	432
0.8-0.85	64
0.85-0.9	45
0.9-0.95	24
0.95-1	18

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 NPC148104 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	309
0.1-0.2	2514
0.2-0.3	3897
0.3-0.4	1688
0.4-0.5	405
0.5-0.6	279
0.6-0.7	48
0.7-0.8	10
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