NPASS Compound

Structure

NPC219225 OpenBabel06302216112D 29 30 0 0 1 0 0 0 0 0999 V2000 -3.2616 -2.7903 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2616 -2.7903 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7616 -1.9243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2616 -1.0583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7616 -1.9243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2616 -1.0583 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2616 -2.7903 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7384 -2.7903 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.3262 -3.5993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2773 -3.2903 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2773 -2.2903 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 2.8650 -1.4813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2773 -0.6723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3262 -0.9813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5000 0.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 0.1340 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 1.8660 0.0000 O 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 0.0000 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 1.8660 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 1.3262 -1.9813 0.0000 C 0 0 2 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 29 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 29 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 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 2 0 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 19 24 1 0 0 0 0 19 28 1 1 0 0 0 20 21 1 6 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 24 27 1 0 0 0 0 29 14 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	411.23
Volume:	416.642
LogP:	1.813
LogD:	1.851
LogS:	-2.079
# Rotatable Bonds:	10
TPSA:	105.53
# H-Bond Aceptor:	8
# H-Bond Donor:	2
# Rings:	2
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.346
Synthetic Accessibility Score:	4.646
Fsp3:	0.714
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-4.722
MDCK Permeability:	5.185115151107311e-05
Pgp-inhibitor:	0.929
Pgp-substrate:	0.007
Human Intestinal Absorption (HIA):	0.032
20% Bioavailability (F20%):	0.64
30% Bioavailability (F30%):	0.976

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.242
Plasma Protein Binding (PPB):	34.26508712768555%
Volume Distribution (VD):	1.239
Pgp-substrate:	51.926124572753906%

ADMET: Metabolism

CYP1A2-inhibitor:	0.023
CYP1A2-substrate:	0.079
CYP2C19-inhibitor:	0.039
CYP2C19-substrate:	0.717
CYP2C9-inhibitor:	0.023
CYP2C9-substrate:	0.081
CYP2D6-inhibitor:	0.046
CYP2D6-substrate:	0.159
CYP3A4-inhibitor:	0.095
CYP3A4-substrate:	0.432

ADMET: Excretion

Clearance (CL):	5.103
Half-life (T1/2):	0.766

ADMET: Toxicity

hERG Blockers:	0.025
Human Hepatotoxicity (H-HT):	0.46
Drug-inuced Liver Injury (DILI):	0.52
AMES Toxicity:	0.452
Rat Oral Acute Toxicity:	0.039
Maximum Recommended Daily Dose:	0.391
Skin Sensitization:	0.097
Carcinogencity:	0.934
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.324

Download Data

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

Natural Product: NPC219225

Natural Product ID:	NPC219225
*Common Name:**	QHOZSLCIKHUPSU-GTZNJGJUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QHOZSLCIKHUPSU-GTZNJGJUSA-N
Standard InCHI:	InChI=1S/C21H33NO7/c1-7-13(2)18(23)29-16-9-11-22-10-8-15(17(16)22)12-28-19(24)21(26,14(3)27-6)20(4,5)25/h7-8,14,16-17,25-26H,9-12H2,1-6H3/b13-7-/t14-,16+,17-,21+/m1/s1
SMILES:	C/C=C(/C)C(=O)O[C@H]1CCN2CC=C(COC(=O)[C@@]([C@@H](C)OC)(C(C)(C)O)O)[C@H]12
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	6325507
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives

*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
NPO25275	Cynoglossum officinale	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17542	Aconitum orientale	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO149	Heliotropium europaeum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9626	Aconitum finetianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2379	Senecio oryzetorum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25821	Delphinium cashmerianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23223	Symphytum officinale	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4002	Lappula intermedia	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8442	Heliotropium curassavicum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10915	Heliotropium hirsutum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23501	Symphytum asperum	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18256	Aconitum excelsum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2379	Senecio oryzetorum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23223	Symphytum officinale	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO149	Heliotropium europaeum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25821	Delphinium cashmerianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4002	Lappula intermedia	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23501	Symphytum asperum	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9626	Aconitum finetianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10915	Heliotropium hirsutum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17542	Aconitum orientale	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18256	Aconitum excelsum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25275	Cynoglossum officinale	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8442	Heliotropium curassavicum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23223	Symphytum officinale	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2379	Senecio oryzetorum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9626	Aconitum finetianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25275	Cynoglossum officinale	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO149	Heliotropium europaeum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO149	Heliotropium europaeum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18256	Aconitum excelsum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10915	Heliotropium hirsutum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23501	Symphytum asperum	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25821	Delphinium cashmerianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17542	Aconitum orientale	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4002	Lappula intermedia	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25275	Cynoglossum officinale	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23223	Symphytum officinale	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9626	Aconitum finetianum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7915	Simarouba amara	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8442	Heliotropium curassavicum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10701	Indigofera aspalathoides	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2379	Senecio oryzetorum	Species	Asteraceae	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 NPC219225 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	93
0.1-0.2	641
0.2-0.3	5625
0.3-0.4	21448
0.4-0.5	10867
0.5-0.6	3572
0.6-0.7	412
0.7-0.8	23
0.8-0.85	1
0.85-0.9	6
0.9-0.95	9
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 NPC219225 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	88
0.1-0.2	547
0.2-0.3	3140
0.3-0.4	3964
0.4-0.5	1175
0.5-0.6	232
0.6-0.7	3
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
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