NPASS Compound

Structure

NPC181218 OpenBabel06302215142D 33 35 0 0 1 0 0 0 0 0999 V2000 2.6583 -4.0888 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6582 -4.0738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1452 -3.2004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1450 -3.1854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6323 -2.3419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1192 -1.4685 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6324 -2.3569 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1195 -1.4985 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5125 -0.5789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7594 0.0790 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9010 -0.4339 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0870 -0.2794 0.0000 C 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 0.5000 -2.1906 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9339 -3.0916 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 -2.1906 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1235 -1.4088 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9010 -0.4339 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7594 0.0790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8491 1.0750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5125 -0.5789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4874 -0.3564 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1195 -1.4985 0.0000 O 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 -0.0000 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9339 -3.0916 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8491 1.0750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7564 1.4953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5741 0.9197 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8461 2.4913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7534 2.9117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5711 2.3361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8431 3.9077 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 3 4 1 0 0 0 0 3 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 8 7 1 6 0 0 0 8 9 1 0 0 0 0 8 13 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 27 1 0 0 0 0 11 24 1 0 0 0 0 11 12 1 0 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 16 26 1 1 0 0 0 17 18 1 0 0 0 0 17 23 1 6 0 0 0 18 19 1 0 0 0 0 18 24 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 24 25 1 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 28 30 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 31 33 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	464.24
Volume:	472.426
LogP:	2.967
LogD:	2.338
LogS:	-3.713
# Rotatable Bonds:	7
TPSA:	119.36
# H-Bond Aceptor:	8
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.361
Synthetic Accessibility Score:	5.091
Fsp3:	0.72
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.865
MDCK Permeability:	6.19944985373877e-05
Pgp-inhibitor:	0.911
Pgp-substrate:	0.007
Human Intestinal Absorption (HIA):	0.015
20% Bioavailability (F20%):	0.012
30% Bioavailability (F30%):	0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.173
Plasma Protein Binding (PPB):	67.05113983154297%
Volume Distribution (VD):	0.789
Pgp-substrate:	17.321929931640625%

ADMET: Metabolism

CYP1A2-inhibitor:	0.098
CYP1A2-substrate:	0.081
CYP2C19-inhibitor:	0.064
CYP2C19-substrate:	0.396
CYP2C9-inhibitor:	0.591
CYP2C9-substrate:	0.116
CYP2D6-inhibitor:	0.009
CYP2D6-substrate:	0.047
CYP3A4-inhibitor:	0.644
CYP3A4-substrate:	0.25

ADMET: Excretion

Clearance (CL):	8.315
Half-life (T1/2):	0.881

ADMET: Toxicity

hERG Blockers:	0.094
Human Hepatotoxicity (H-HT):	0.911
Drug-inuced Liver Injury (DILI):	0.822
AMES Toxicity:	0.017
Rat Oral Acute Toxicity:	0.448
Maximum Recommended Daily Dose:	0.188
Skin Sensitization:	0.496
Carcinogencity:	0.047
Eye Corrosion:	0.009
Eye Irritation:	0.02
Respiratory Toxicity:	0.937

Download Data

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

Natural Product: NPC181218

Natural Product ID:	NPC181218
*Common Name:**	IQWHMZWVTALWMV-PMZTZJADSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IQWHMZWVTALWMV-PMZTZJADSA-N
Standard InCHI:	InChI=1S/C25H36O8/c1-8-12(4)23(29)31-15-10-16(32-17(26)9-11(2)3)25(7)19(15)14(6)20(27)21-18(22(25)28)13(5)24(30)33-21/h8,11,14-16,18-22,27-28H,5,9-10H2,1-4,6-7H3/b12-8-/t14-,15-,16+,18+,19+,20+,21+,22+,25+/m0/s1
SMILES:	C/C=C(/C)C(=O)O[C@H]1C[C@H]([C@]2(C)[C@@H]1[C@H](C)[C@H]([C@H]1[C@@H](C(=C)C(=O)O1)[C@H]2O)O)OC(=O)CC(C)C
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]
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[TCMID]
NPO17767	Artocarpus heterophyllus	Species	Moraceae	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]
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]
NPO5073	Fontainea picrosperma	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2282	Ageratina altissima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25921	Papaver nudicaule	Species	Papaveraceae	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]

☑ 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 NPC181218 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	268
0.1-0.2	1549
0.2-0.3	5668
0.3-0.4	11704
0.4-0.5	11276
0.5-0.6	7260
0.6-0.7	3896
0.7-0.8	919
0.8-0.85	108
0.85-0.9	43
0.9-0.95	6
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 NPC181218 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	294
0.1-0.2	2287
0.2-0.3	3819
0.3-0.4	1886
0.4-0.5	512
0.5-0.6	243
0.6-0.7	99
0.7-0.8	8
0.8-0.85	2
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