NPASS Compound

Structure

NPC66172 OpenBabel06302216112D 31 34 0 0 1 0 0 0 0 0999 V2000 -2.5318 -0.4887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5315 -1.4635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3756 -1.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6871 -1.9507 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6868 -2.9256 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8430 -1.4630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0015 -1.9502 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8456 -1.4626 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6900 -1.9498 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8453 -0.4877 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6891 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6889 0.9758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9753 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8456 1.4630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8459 2.4388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6912 2.9265 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6914 3.9265 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5362 2.4384 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3809 2.9260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2253 2.4379 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2250 1.4620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3803 0.9743 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5359 1.4625 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5356 0.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6906 0.9748 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6903 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8450 -0.4882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0003 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0916 2.9375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5365 3.4384 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 2 4 1 0 0 0 0 4 5 1 6 0 0 0 4 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 6 0 0 0 10 8 1 6 0 0 0 10 11 1 0 0 0 0 10 28 1 0 0 0 0 11 12 1 0 0 0 0 13 12 1 6 0 0 0 13 14 1 0 0 0 0 13 28 1 0 0 0 0 14 25 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 18 23 1 0 0 0 0 18 19 1 0 0 0 0 18 31 1 1 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 30 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 23 25 1 0 0 0 0 25 26 1 6 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	592.3
Volume:	629.567
LogP:	6.71
LogD:	2.148
LogS:	-3.213
# Rotatable Bonds:	11
TPSA:	135.04
# H-Bond Aceptor:	8
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.17
Synthetic Accessibility Score:	4.843
Fsp3:	0.514
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	2
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.844
MDCK Permeability:	2.231116195616778e-05
Pgp-inhibitor:	0.955
Pgp-substrate:	0.711
Human Intestinal Absorption (HIA):	0.275
20% Bioavailability (F20%):	0.762
30% Bioavailability (F30%):	0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.024
Plasma Protein Binding (PPB):	97.77619171142578%
Volume Distribution (VD):	0.577
Pgp-substrate:	0.893416702747345%

ADMET: Metabolism

CYP1A2-inhibitor:	0.055
CYP1A2-substrate:	0.601
CYP2C19-inhibitor:	0.524
CYP2C19-substrate:	0.676
CYP2C9-inhibitor:	0.864
CYP2C9-substrate:	0.983
CYP2D6-inhibitor:	0.808
CYP2D6-substrate:	0.094
CYP3A4-inhibitor:	0.869
CYP3A4-substrate:	0.791

ADMET: Excretion

Clearance (CL):	7.014
Half-life (T1/2):	0.093

ADMET: Toxicity

hERG Blockers:	0.007
Human Hepatotoxicity (H-HT):	0.462
Drug-inuced Liver Injury (DILI):	0.931
AMES Toxicity:	0.002
Rat Oral Acute Toxicity:	0.981
Maximum Recommended Daily Dose:	0.417
Skin Sensitization:	0.117
Carcinogencity:	0.26
Eye Corrosion:	0.003
Eye Irritation:	0.138
Respiratory Toxicity:	0.707

Download Data

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

Natural Product: NPC66172

Natural Product ID:	NPC66172
*Common Name:**	KAIVGEVOBNIWLR-QIBDZGQISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KAIVGEVOBNIWLR-QIBDZGQISA-N
Standard InCHI:	InChI=1S/C28H44O3/c1-17(2)18(3)7-8-19(4)22-9-10-23-21-15-25(30)28(31)16-20(29)11-14-27(28,6)24(21)12-13-26(22,23)5/h7-8,15,17-20,22-24,29,31H,9-14,16H2,1-6H3/b8-7+/t18-,19+,20-,22+,23-,24-,26+,27+,28-/m0/s1
SMILES:	CC(C)[C@@H](C)/C=C/[C@@H](C)[C@H]1CC[C@H]2C3=CC(=O)[C@]4(C[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	15340727
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0003567] Ergostane steroids [CHEMONTID:0001403] Ergosterols and derivatives

*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
NPO3499	Macaranga conifera	Species	Euphorbiaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/S0031-9422(02)00378-3]
NPO14094	Aspergillus ochraceus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11170686]
NPO14094	Aspergillus ochraceus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16156520]
NPO16239	Rhodiola rosea	Species	Crassulaceae	Eukaryota	roots	n.a.	n.a.	PMID[19729316]
NPO14094	Aspergillus ochraceus	Species	Aspergillaceae	Eukaryota	n.a.	mycelium	n.a.	PMID[21043476]
NPO3499	Macaranga conifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21275386]
NPO8301	Erythrina suberosa	Species	Fabaceae	Eukaryota	n.a.	seed	n.a.	PMID[5348524]
NPO3499	Macaranga conifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8301	Erythrina suberosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3499	Macaranga conifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8301	Erythrina suberosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16239	Rhodiola rosea	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8301	Erythrina suberosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO370	Rhizophora apiculata	Species	Rhizophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9378	Halocynthia aurantium	Species	Pyuridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6631	Elaeagnus glabra	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8301	Erythrina suberosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14503	Glycosmis craibii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1779	Sargassum kjellmanianum	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11051	Nicotiana cavicola	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17323	Murex brandaris	Species	Muricidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO155	Artemisia lanata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5443	Coltricia cinnamomea	Species	Hymenochaetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5288	Stomatanthes corumbensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3499	Macaranga conifera	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14094	Aspergillus ochraceus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2271	Cassia reticulata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28869	Neonectria obtusispora	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28832	Baccharoides adoensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8684	Nymphaea ampla	Species	Nymphaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12752	Yucca baccata	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4483	Ganonema farinosum	Species	Liagoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19426	Diospyros ferrea	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17677	Eremophila latrobei	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16239	Rhodiola rosea	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24388	Pinus pinaster	Species	Pinaceae	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	2

Activity Type	# Activity
Cell Line	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	GI	=	100.0	%	PMID[491189]
NPT65	Cell Line	HepG2	Homo sapiens	GI	=	100.0	%	PMID[491189]

☑ 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 NPC66172 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	189
0.1-0.2	1182
0.2-0.3	4651
0.3-0.4	10074
0.4-0.5	11875
0.5-0.6	6394
0.6-0.7	5518
0.7-0.8	2513
0.8-0.85	209
0.85-0.9	85
0.9-0.95	4
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 NPC66172 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	163
0.1-0.2	1463
0.2-0.3	4004
0.3-0.4	2345
0.4-0.5	689
0.5-0.6	164
0.6-0.7	125
0.7-0.8	119
0.8-0.85	52
0.85-0.9	26
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