NPASS Compound

Structure

NPC66306 OpenBabel06302215592D 23 25 0 0 1 0 0 0 0 0999 V2000 -2.0701 -1.2875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8749 -1.6077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.7328 0.0000 N 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 -0.8749 0.8749 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7328 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0992 0.6346 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4815 -0.5421 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7188 -0.5421 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1012 0.6346 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4676 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4676 -0.7328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1012 -1.3674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4666 -1.7338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7338 -1.7338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0992 -1.3674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7328 -0.7328 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.9279 -1.0530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6627 0.3202 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1002 1.3619 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.1002 2.5992 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6629 1.7371 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8985 1.8018 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 17 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 6 17 1 0 0 0 0 6 7 2 0 0 0 0 7 20 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 10 20 1 0 0 0 0 10 22 1 1 0 0 0 11 12 1 0 0 0 0 11 19 1 1 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 17 1 0 0 0 0 17 18 1 6 0 0 0 20 21 1 6 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	325.19
Volume:	326.594
LogP:	1.856
LogD:	1.835
LogS:	-2.797
# Rotatable Bonds:	2
TPSA:	76.07
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.77
Synthetic Accessibility Score:	5.788
Fsp3:	0.882
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.685
MDCK Permeability:	2.3885941118351184e-05
Pgp-inhibitor:	0.059
Pgp-substrate:	0.116
Human Intestinal Absorption (HIA):	0.012
20% Bioavailability (F20%):	0.495
30% Bioavailability (F30%):	0.851

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.751
Plasma Protein Binding (PPB):	63.77855682373047%
Volume Distribution (VD):	1.433
Pgp-substrate:	45.425846099853516%

ADMET: Metabolism

CYP1A2-inhibitor:	0.013
CYP1A2-substrate:	0.873
CYP2C19-inhibitor:	0.044
CYP2C19-substrate:	0.882
CYP2C9-inhibitor:	0.026
CYP2C9-substrate:	0.039
CYP2D6-inhibitor:	0.008
CYP2D6-substrate:	0.127
CYP3A4-inhibitor:	0.145
CYP3A4-substrate:	0.589

ADMET: Excretion

Clearance (CL):	9.79
Half-life (T1/2):	0.689

ADMET: Toxicity

hERG Blockers:	0.007
Human Hepatotoxicity (H-HT):	0.19
Drug-inuced Liver Injury (DILI):	0.773
AMES Toxicity:	0.481
Rat Oral Acute Toxicity:	0.685
Maximum Recommended Daily Dose:	0.351
Skin Sensitization:	0.225
Carcinogencity:	0.958
Eye Corrosion:	0.004
Eye Irritation:	0.023
Respiratory Toxicity:	0.112

Download Data

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

Natural Product: NPC66306

Natural Product ID:	NPC66306
*Common Name:**	SJSPSHPVPXPTPG-WCYNIRFRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SJSPSHPVPXPTPG-WCYNIRFRSA-N
Standard InCHI:	InChI=1S/C17H27NO5/c1-4-18-15(21)13-11-10-23-17(22-3,14(11)20)12(19)8-6-5-7-9-16(13,18)2/h12,14,19-20H,4-10H2,1-3H3/b13-11-/t12-,14-,16+,17-/m0/s1
SMILES:	CCN1C(=O)/C/2=C/3CO[C@@]([C@H](CCCCC[C@@]12C)O)([C@H]3O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	24813209
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000254] Ethers [CHEMONTID:0001656] Acetals [CHEMONTID:0004472] Ketals

*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
NPO1528	Dalea elegans	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21561780]
NPO9064	Cirsium arvense	Species	Asteraceae	Eukaryota	n.a.	fruit	n.a.	PMID[22396124]
NPO11062	Euonymus grandiflorus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8685	Hymenocallis arenicola	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11062	Euonymus grandiflorus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4471	Blumea densiflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO480	Hygrophila erecta	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24513	Streptomyces cyaneofuscatus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO9525	Relicina samoensis	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO743	Wardomyces inflatus	Species	Microascaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11062	Euonymus grandiflorus	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9064	Cirsium arvense	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6024	Cratoxylum formosum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8685	Hymenocallis arenicola	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1785	Corallina rubens	Species	Corallinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1528	Dalea elegans	Species	Fabaceae	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
Others	1

Activity Type	# Activity
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT176	Organism	Artemia salina	Artemia salina	mortality	=	24.0	%	PMID[456021]

☑ 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 NPC66306 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 NPC66306 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