NPASS Compound

Structure

NPC482577 OpenBabel06302215102D 26 28 0 0 1 0 0 0 0 0999 V2000 1.3660 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -2.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.2321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.9641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0622 -0.6340 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -0.6340 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 7.4282 -2.0000 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -3.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6962 -5.0000 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 6.1962 -4.1340 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -6.0000 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 1 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 26 1 0 0 0 0 8 17 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 15 1 0 0 0 0 11 12 1 0 0 0 0 11 13 1 0 0 0 0 11 14 1 0 0 0 0 15 16 2 0 0 0 0 16 21 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 24 1 0 0 0 0 22 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	378.12
Volume:	330.926
LogP:	3.622
LogD:	3.634
LogS:	-2.372
# Rotatable Bonds:	4
TPSA:	45.15
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.759
Synthetic Accessibility Score:	3.492
Fsp3:	0.471
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.123
MDCK Permeability:	1.2024042007396929e-05
Pgp-inhibitor:	0.892
Pgp-substrate:	0.513
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.133
30% Bioavailability (F30%):	0.03

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.414
Plasma Protein Binding (PPB):	87.64249420166016%
Volume Distribution (VD):	3.145
Pgp-substrate:	5.5380659103393555%

ADMET: Metabolism

CYP1A2-inhibitor:	0.405
CYP1A2-substrate:	0.915
CYP2C19-inhibitor:	0.256
CYP2C19-substrate:	0.883
CYP2C9-inhibitor:	0.048
CYP2C9-substrate:	0.065
CYP2D6-inhibitor:	0.911
CYP2D6-substrate:	0.587
CYP3A4-inhibitor:	0.226
CYP3A4-substrate:	0.574

ADMET: Excretion

Clearance (CL):	3.74
Half-life (T1/2):	0.027

ADMET: Toxicity

hERG Blockers:	0.857
Human Hepatotoxicity (H-HT):	0.945
Drug-inuced Liver Injury (DILI):	0.114
AMES Toxicity:	0.089
Rat Oral Acute Toxicity:	0.935
Maximum Recommended Daily Dose:	0.954
Skin Sensitization:	0.037
Carcinogencity:	0.084
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.898

Download Data

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

Natural Product: NPC482577

Natural Product ID:	NPC482577
*Common Name:**	WESWYMRNZNDGBX-YLCXCWDSSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WESWYMRNZNDGBX-YLCXCWDSSA-N
Standard InCHI:	InChI=1S/C17H16F6N2O.ClH/c18-16(19,20)11-5-3-4-9-10(15(26)12-6-1-2-7-24-12)8-13(17(21,22)23)25-14(9)11;/h3-5,8,12,15,24,26H,1-2,6-7H2;1H/t12-,15+;/m1./s1
SMILES:	C1CCN[C@H](C1)[C@H](c1cc(C(F)(F)F)nc2c1cccc2C(F)(F)F)O.Cl
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	65329
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001253] Quinolines and derivatives [CHEMONTID:0004538] 4-quinolinemethanols

*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
NPO40511	Favolaschia calocera BCC 36684	Strain	Favolaschiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32193929]
NPO40512	Favolaschia sp. BCC 18686	Strain	Favolaschiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32193929]
NPO40139	Ganoderma colossus	Species	Polyporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32639735]

☑ 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
EC50	2
IC50	7
Others	35

Activity Type	# Activity
Cell Line	3
Individual Protein	7
Organism	34

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT65	Cell Line	HepG2	Homo sapiens	Inhibition	=	29.0	%	PMID[20485427]
NPT65	Cell Line	HepG2	Homo sapiens	Inhibition	=	0.0	%	PMID[20485427]
NPT1229	Cell Line	Huh-7	Homo sapiens	CC50	>	6250.0	nM	PMID[18579783]
NPT1217	Individual Protein	Botulinum neurotoxin type A	Clostridium botulinum	Inhibition	=	28.0	%	PMID[23815186]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Inhibition	=	99.0	%	PMID[20485427]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Inhibition	=	7.0	%	PMID[20485427]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Inhibition	=	96.0	%	PMID[20485427]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Inhibition	=	0.0	%	PMID[20485427]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	EC50	=	2.372	nM	PMID[18579783]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	EC50	=	51.7	nM	PMID[18579783]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC90	=	75.22	nM	PMID[23815186]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	27.98	nM	PMID[23815186]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC90	=	132.73	nM	PMID[23815186]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	51.12	nM	PMID[23815186]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	65.55	nM	PMID[23815186]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC90	=	43.65	nM	PMID[23815186]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	19.98	nM	PMID[23815186]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC90	=	18.09	nM	PMID[23815186]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	6.5	nM	PMID[23815186]
NPT942	Individual Protein	Glucose transporter	Homo sapiens	Inhibition	=	13.61	%	DOI[10.6019/CHEMBL3433997]
NPT942	Individual Protein	Glucose transporter	Homo sapiens	Inhibition	=	1.21	%	DOI[10.6019/CHEMBL3433997]
NPT943	Individual Protein	Hexose transporter 1	Plasmodium falciparum	Inhibition	=	8.31	%	DOI[10.6019/CHEMBL3433997]
NPT943	Individual Protein	Hexose transporter 1	Plasmodium falciparum	Inhibition	=	0.88	%	DOI[10.6019/CHEMBL3433997]
NPT944	Individual Protein	Glucose transporter	Leishmania mexicana	Inhibition	=	7.19	%	DOI[10.6019/CHEMBL3433997]
NPT944	Individual Protein	Glucose transporter	Leishmania mexicana	Inhibition	=	1.05	%	DOI[10.6019/CHEMBL3433997]
NPT20	Organism	Candida albicans	Candida albicans	Inhibition	=	5.35	%	DOI[10.6019/CHEMBL4296181]
NPT85	Organism	Filobasidiella neoformans	Cryptococcus neoformans	Inhibition	=	-9.28	%	DOI[10.6019/CHEMBL4296181]
NPT19	Organism	Escherichia coli	Escherichia coli	Inhibition	=	7.08	%	DOI[10.6019/CHEMBL4296181]
NPT173	Organism	Klebsiella pneumoniae	Klebsiella pneumoniae	Inhibition	=	14.04	%	DOI[10.6019/CHEMBL4296181]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Inhibition	=	14.68	%	DOI[10.6019/CHEMBL4296181]
NPT747	Organism	Acinetobacter baumannii	Acinetobacter baumannii	Inhibition	=	32.5	%	DOI[10.6019/CHEMBL4296181]
NPT2922	Organism	Staphylococcus aureus subsp. aureus	Staphylococcus aureus subsp. aureus	Inhibition	=	36.85	%	DOI[10.6019/CHEMBL4296181]
NPT20	Organism	Candida albicans	Candida albicans	Inhibition	=	6.48	%	DOI[10.6019/CHEMBL4296181]
NPT85	Organism	Filobasidiella neoformans	Cryptococcus neoformans	Inhibition	=	1.73	%	DOI[10.6019/CHEMBL4296181]
NPT19	Organism	Escherichia coli	Escherichia coli	Inhibition	=	15.86	%	DOI[10.6019/CHEMBL4296181]
NPT173	Organism	Klebsiella pneumoniae	Klebsiella pneumoniae	Inhibition	=	-6.56	%	DOI[10.6019/CHEMBL4296181]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Inhibition	=	18.63	%	DOI[10.6019/CHEMBL4296181]
NPT747	Organism	Acinetobacter baumannii	Acinetobacter baumannii	Inhibition	=	13.75	%	DOI[10.6019/CHEMBL4296181]
NPT2922	Organism	Staphylococcus aureus subsp. aureus	Staphylococcus aureus subsp. aureus	Inhibition	=	45.36	%	DOI[10.6019/CHEMBL4296181]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	52.0	nM	PMID[32193929]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	>	10.0	ug.mL-1	PMID[32639735]

☑ 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 NPC482577 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	391
0.1-0.2	2193
0.2-0.3	13022
0.3-0.4	16902
0.4-0.5	5321
0.5-0.6	2873
0.6-0.7	1717
0.7-0.8	272
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	3

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 NPC482577 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	202
0.1-0.2	575
0.2-0.3	843
0.3-0.4	1261
0.4-0.5	2596
0.5-0.6	2648
0.6-0.7	905
0.7-0.8	111
0.8-0.85	6
0.85-0.9	0
0.9-0.95	0
0.95-1	3

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