NPASS Compound

Structure

NPC159201 OpenBabel06302215342D 30 35 0 0 1 0 0 0 0 0999 V2000 -0.8436 1.5086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8435 0.4868 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6868 -0.0002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6867 -0.9741 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8432 -1.4609 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8431 -2.4348 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7279 -2.9458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0004 -2.9217 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0004 -3.8962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8438 -4.3831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6877 -3.8961 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6876 -2.9216 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5310 -2.4345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3749 -2.9215 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3750 -3.8960 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2189 -4.3829 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0622 -3.8959 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.0622 -2.9214 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9056 -2.4344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9056 -1.4605 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.0622 -0.9736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2188 -1.4605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2188 -2.4344 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3527 -1.9344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7905 -0.9497 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9283 -4.3959 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8437 -2.4346 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8436 -1.4607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0001 -0.9739 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 30 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 6 0 0 0 5 6 1 0 0 0 0 5 29 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 8 9 1 6 0 0 0 8 27 1 0 0 0 0 9 10 1 0 0 0 0 11 10 1 6 0 0 0 11 12 1 0 0 0 0 11 15 1 0 0 0 0 12 13 1 6 0 0 0 12 27 1 0 0 0 0 14 13 1 6 0 0 0 14 15 1 0 0 0 0 14 23 1 0 0 0 0 15 16 1 1 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 26 1 6 0 0 0 18 19 1 6 0 0 0 18 23 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 25 1 6 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 6 0 0 0 27 28 1 1 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	415.35
Volume:	452.787
LogP:	5.679
LogD:	5.213
LogS:	-4.937
# Rotatable Bonds:	0
TPSA:	43.7
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.609
Synthetic Accessibility Score:	4.981
Fsp3:	1.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.833
MDCK Permeability:	2.129640051862225e-05
Pgp-inhibitor:	0.78
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.053
20% Bioavailability (F20%):	0.789
30% Bioavailability (F30%):	0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.263
Plasma Protein Binding (PPB):	82.39936828613281%
Volume Distribution (VD):	2.749
Pgp-substrate:	3.8205270767211914%

ADMET: Metabolism

CYP1A2-inhibitor:	0.111
CYP1A2-substrate:	0.321
CYP2C19-inhibitor:	0.046
CYP2C19-substrate:	0.905
CYP2C9-inhibitor:	0.084
CYP2C9-substrate:	0.063
CYP2D6-inhibitor:	0.555
CYP2D6-substrate:	0.814
CYP3A4-inhibitor:	0.52
CYP3A4-substrate:	0.678

ADMET: Excretion

Clearance (CL):	15.69
Half-life (T1/2):	0.303

ADMET: Toxicity

hERG Blockers:	0.906
Human Hepatotoxicity (H-HT):	0.281
Drug-inuced Liver Injury (DILI):	0.892
AMES Toxicity:	0.25
Rat Oral Acute Toxicity:	0.015
Maximum Recommended Daily Dose:	0.505
Skin Sensitization:	0.972
Carcinogencity:	0.383
Eye Corrosion:	0.992
Eye Irritation:	0.537
Respiratory Toxicity:	0.872

Download Data

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

Natural Product: NPC159201

Natural Product ID:	NPC159201
*Common Name:**	NEMWYOKGHGSVSC-DZYYLIMLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NEMWYOKGHGSVSC-DZYYLIMLSA-N
Standard InCHI:	InChI=1S/C27H45NO2/c1-15-4-7-25-16(2)18-5-6-19-20(22(18)14-28(25)13-15)11-23-21(19)12-26(30)24-10-17(29)8-9-27(23,24)3/h15-26,29-30H,4-14H2,1-3H3/t15-,16+,17-,18+,19+,20+,21-,22+,23-,24+,25-,26+,27+/m0/s1
SMILES:	C[C@H]1CC[C@H]2[C@H](C)[C@H]3CC[C@@H]4[C@@H](C[C@H]5[C@H]4C[C@H]([C@H]4C[C@H](CC[C@]54C)O)O)[C@@H]3CN2C1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5316983
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002724] Steroidal alkaloids [CHEMONTID:0002729] Cerveratrum-type 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
NPO10290	Fritillaria ebeiensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10290	Fritillaria ebeiensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25941	Garcinia yunnanensis	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10290	Fritillaria ebeiensis	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26833	Ichnocarpus frutescens	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23477	Anabaena torulosa	Species	0stocaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO26765	Litsea pedunculata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26282	Phebalium ovatifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25749	Kielmeyera argentea	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25253	Corydalis caseana	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28973	Rhytisma fulvum	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26065	Elaeocarpus archboldianus	Species	Elaeocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26340	Chione venosa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26096	Jatropha multiloba	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25300	Senecio ruderalis	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

Activity Type	# Activity
IC50	2
Others	1

Activity Type	# Activity
Individual Protein	2
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT66	Individual Protein	Acetylcholinesterase	Electrophorus electricus	IC50	=	45830.0	nM	PMID[514998]
NPT67	Individual Protein	Cholinesterase	Equus caballus	IC50	=	18620.0	nM	PMID[514998]
NPT2	Others	Unspecified		Ratio IC50	=	0.41	n.a.	PMID[514998]

☑ 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 NPC159201 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	146
0.1-0.2	4000
0.2-0.3	19443
0.3-0.4	9605
0.4-0.5	5005
0.5-0.6	3430
0.6-0.7	968
0.7-0.8	94
0.8-0.85	3
0.85-0.9	1
0.9-0.95	0
0.95-1	2

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 NPC159201 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	101
0.1-0.2	1934
0.2-0.3	4917
0.3-0.4	1554
0.4-0.5	455
0.5-0.6	132
0.6-0.7	44
0.7-0.8	13
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