NPASS Compound

Structure

NPC46935 OpenBabel06302215542D 27 31 0 0 1 0 0 0 0 0999 V2000 -8.7431 -1.9690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0629 -2.7020 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.0880 -2.4795 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4078 -3.2126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4329 -2.9900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8696 -3.8163 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8724 -3.8910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1922 -3.1580 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.3412 -2.1691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4752 -1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6092 -2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7431 -1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7431 -0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6092 -0.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4752 -0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3412 -0.1691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3412 0.8309 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4752 1.3309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2072 -0.6691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2072 -1.6691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1381 -2.0345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8183 -1.3014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7932 -1.5239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4734 -0.7909 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4013 0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4067 0.9135 0.0000 C 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 2 1 0 0 0 0 2 3 1 0 0 0 0 3 23 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 21 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 20 1 0 0 0 0 10 15 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 13 27 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 25 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 6 0 0 0 16 19 1 0 0 0 0 17 18 1 0 0 0 0 20 19 1 6 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	371.14
Volume:	359.613
LogP:	1.232
LogD:	2.404
LogS:	-3.193
# Rotatable Bonds:	2
TPSA:	78.41
# H-Bond Aceptor:	7
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.84
Synthetic Accessibility Score:	4.044
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.903
MDCK Permeability:	1.3738082088821102e-05
Pgp-inhibitor:	0.052
Pgp-substrate:	0.982
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.957
Plasma Protein Binding (PPB):	77.22850799560547%
Volume Distribution (VD):	1.48
Pgp-substrate:	11.957718849182129%

ADMET: Metabolism

CYP1A2-inhibitor:	0.156
CYP1A2-substrate:	0.836
CYP2C19-inhibitor:	0.349
CYP2C19-substrate:	0.851
CYP2C9-inhibitor:	0.072
CYP2C9-substrate:	0.581
CYP2D6-inhibitor:	0.945
CYP2D6-substrate:	0.902
CYP3A4-inhibitor:	0.87
CYP3A4-substrate:	0.75

ADMET: Excretion

Clearance (CL):	8.058
Half-life (T1/2):	0.238

ADMET: Toxicity

hERG Blockers:	0.37
Human Hepatotoxicity (H-HT):	0.566
Drug-inuced Liver Injury (DILI):	0.33
AMES Toxicity:	0.941
Rat Oral Acute Toxicity:	0.728
Maximum Recommended Daily Dose:	0.948
Skin Sensitization:	0.717
Carcinogencity:	0.626
Eye Corrosion:	0.003
Eye Irritation:	0.009
Respiratory Toxicity:	0.882

Download Data

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

Natural Product: NPC46935

Natural Product ID:	NPC46935
*Common Name:**	YLUOVOKBMSLYGX-HBFSDRIKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YLUOVOKBMSLYGX-HBFSDRIKSA-N
Standard InCHI:	InChI=1S/C20H21NO6/c1-23-15-7-10-5-6-21-17-11-3-4-14-19(26-9-25-14)16(11)20(24-2)27-18(17)12(10)8-13(15)22/h3-4,7-8,17-18,20-22H,5-6,9H2,1-2H3/t17-,18+,20+/m1/s1
SMILES:	COc1cc2CCN[C@@H]3c4ccc5c(c4[C@@H](OC)O[C@H]3c2cc1O)OCO5
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	12309641
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0002658] Rhoeadine alkaloids

*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
NPO14337	Ecklonia stolonifera	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12913249]
NPO9498	Papaver somniferum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15019787]
NPO9498	Papaver somniferum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22029392]
NPO9498	Papaver somniferum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23517479]
NPO9498	Papaver somniferum	Species	Papaveraceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO9498	Papaver somniferum	Species	Papaveraceae	Eukaryota	Latex Exudate	n.a.	n.a.	Database[FooDB]
NPO9498	Papaver somniferum	Species	Papaveraceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO9498	Papaver somniferum	Species	Papaveraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO14337	Ecklonia stolonifera	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9498	Papaver somniferum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9498	Papaver somniferum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14337	Ecklonia stolonifera	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9498	Papaver somniferum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9498	Papaver somniferum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16169	Sedum altissimum	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6137	Lepista glaucocana	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7312	Aplidium multiplicatum	Species	Polyclinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15455	Karwinskia johnstonii	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2466	Aloe microstigma	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13235	Berberis chitria	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16670	Centaurea sclerolepis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14659	Cereus pecten-aboriginum	Species	Sagartiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15522	Michelia fuscata	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2826	Pseudocercospora cruenta	Species	Mycosphaerellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12540	Fuligo septica	Species	Physaraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10176	Chrozophora prostrata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7063	Gentianella amarella	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14337	Ecklonia stolonifera	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26740	Tolypothrix distorta	Species	Tolypothrichaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO9498	Papaver somniferum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15415	Othonna obtusiloba	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26963	Sarcocapnos enneaphylla	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9511	Ranunculus serbicus	Species	Ranunculaceae	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 NPC46935 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	301
0.1-0.2	1423
0.2-0.3	6103
0.3-0.4	11461
0.4-0.5	6114
0.5-0.6	10715
0.6-0.7	5266
0.7-0.8	1062
0.8-0.85	222
0.85-0.9	22
0.9-0.95	8
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 NPC46935 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	183
0.1-0.2	641
0.2-0.3	1080
0.3-0.4	2251
0.4-0.5	2509
0.5-0.6	1621
0.6-0.7	675
0.7-0.8	186
0.8-0.85	2
0.85-0.9	2
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