NPASS Compound

Structure

NPC316670 OpenBabel06302215182D 22 22 0 0 1 0 0 0 0 0999 V2000 12.9904 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 0 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 0.0000 -3.0000 0.0000 C 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 4 1 0 0 0 0 4 5 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 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 21 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 22 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	307.32
Volume:	371.576
LogP:	8.763
LogD:	4.826
LogS:	-6.97
# Rotatable Bonds:	14
TPSA:	12.36
# H-Bond Aceptor:	1
# H-Bond Donor:	0
# Rings:	1
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.295
Synthetic Accessibility Score:	2.987
Fsp3:	0.952
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.843
MDCK Permeability:	7.8689099609619e-06
Pgp-inhibitor:	0.001
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.375
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.027
Plasma Protein Binding (PPB):	98.00360107421875%
Volume Distribution (VD):	3.208
Pgp-substrate:	0.7983534336090088%

ADMET: Metabolism

CYP1A2-inhibitor:	0.13
CYP1A2-substrate:	0.195
CYP2C19-inhibitor:	0.221
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.1
CYP2C9-substrate:	0.903
CYP2D6-inhibitor:	0.36
CYP2D6-substrate:	0.233
CYP3A4-inhibitor:	0.312
CYP3A4-substrate:	0.072

ADMET: Excretion

Clearance (CL):	3.95
Half-life (T1/2):	0.064

ADMET: Toxicity

hERG Blockers:	0.415
Human Hepatotoxicity (H-HT):	0.102
Drug-inuced Liver Injury (DILI):	0.149
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.036
Maximum Recommended Daily Dose:	0.129
Skin Sensitization:	0.945
Carcinogencity:	0.032
Eye Corrosion:	0.282
Eye Irritation:	0.874
Respiratory Toxicity:	0.712

Download Data

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

Natural Product: NPC316670

Natural Product ID:	NPC316670
*Common Name:**	YMZAXCVACZXRMD-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YMZAXCVACZXRMD-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C21H41N/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-18-21-19-16-17-20(2)22-21/h20H,3-19H2,1-2H3
SMILES:	CCCCCCCCCCCCCCCC1=NC(CCC1)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	70698157
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000089] Pyridines and derivatives [CHEMONTID:0002224] Hydropyridines [CHEMONTID:0001934] Tetrahydropyridines

*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
NPO12977	Solenopsis invicta	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21905650]
NPO12977	Solenopsis invicta	Species	Formicidae	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	8
MIC	3
Others	5

Activity Type	# Activity
Cell Line	2
Organism	14

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1970	Cell Line	THP-1	Homo sapiens	IC50	>	10.0	ug.mL-1	PMID[458232]
NPT1970	Cell Line	THP-1	Homo sapiens	IC90	>	10.0	ug.mL-1	PMID[458232]
NPT85	Organism	Filobasidiella neoformans	Cryptococcus neoformans	IC50	=	6.6	ug.mL-1	PMID[458232]
NPT20	Organism	Candida albicans	Candida albicans	IC50	=	12.4	ug.mL-1	PMID[458232]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	IC50	=	19.4	ug.mL-1	PMID[458232]
NPT633	Organism	Leishmania donovani	Leishmania donovani	IC50	=	5.7	ug.mL-1	PMID[458232]
NPT633	Organism	Leishmania donovani	Leishmania donovani	IC50	>	10.0	ug.mL-1	PMID[458232]
NPT633	Organism	Leishmania donovani	Leishmania donovani	IC50	=	3.1	ug.mL-1	PMID[458232]
NPT1018	Organism	Trypanosoma brucei	Trypanosoma brucei	IC50	=	2.7	ug.mL-1	PMID[458232]
NPT85	Organism	Filobasidiella neoformans	Cryptococcus neoformans	MIC	=	10.0	ug.mL-1	PMID[458232]
NPT20	Organism	Candida albicans	Candida albicans	MIC	=	20.0	ug.mL-1	PMID[458232]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	MIC	=	20.0	ug.mL-1	PMID[458232]
NPT633	Organism	Leishmania donovani	Leishmania donovani	IC90	=	7.9	ug.mL-1	PMID[458232]
NPT633	Organism	Leishmania donovani	Leishmania donovani	IC90	>	10.0	ug.mL-1	PMID[458232]
NPT1018	Organism	Trypanosoma brucei	Trypanosoma brucei	IC90	=	3.6	ug.mL-1	PMID[458232]

☑ 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 NPC316670 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

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 NPC316670 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

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