NPASS Compound

Structure

NPC172373 OpenBabel06302216142D 34 37 0 0 1 0 0 0 0 0999 V2000 1.6894 -3.9082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8438 -4.3965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0019 -3.9082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8475 -4.3964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6931 -3.9082 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5388 -4.3964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6931 -2.9317 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5385 -2.4430 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5384 -1.4661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8466 -1.4662 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -0.9775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8465 -1.4662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8465 -2.4431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7125 -2.9431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0001 -2.9318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8466 -2.4430 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8466 -3.4430 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6930 -0.9775 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6930 -1.9775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5390 -1.4662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3849 -0.9775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3849 -0.0001 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5390 0.4887 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5390 1.4887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6931 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8465 0.4887 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 -0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2510 0.4998 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8437 -5.3729 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0019 -5.8611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6894 -5.8612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6894 -6.8376 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5350 -5.3729 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 2 30 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 1 0 0 0 7 5 1 1 0 0 0 7 8 1 0 0 0 0 7 16 1 0 0 0 0 8 9 1 0 0 0 0 10 9 1 1 0 0 0 10 11 1 0 0 0 0 10 16 1 0 0 0 0 11 27 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 12 18 1 0 0 0 0 13 14 2 0 0 0 0 13 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 1 0 0 0 18 25 1 0 0 0 0 18 19 1 1 0 0 0 18 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 29 1 6 0 0 0 23 24 1 6 0 0 0 23 25 1 0 0 0 0 25 26 1 1 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 30 31 1 6 0 0 0 30 32 1 0 0 0 0 32 33 2 0 0 0 0 32 34 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	242.08
Volume:	226.531
LogP:	-0.509
LogD:	-0.674
LogS:	-2.4
# Rotatable Bonds:	2
TPSA:	100.9
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	2
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.578
Synthetic Accessibility Score:	4.954
Fsp3:	0.727
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.389
MDCK Permeability:	2.4106038836180232e-05
Pgp-inhibitor:	0.002
Pgp-substrate:	0.157
Human Intestinal Absorption (HIA):	0.168
20% Bioavailability (F20%):	0.651
30% Bioavailability (F30%):	0.178

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.837
Plasma Protein Binding (PPB):	28.737178802490234%
Volume Distribution (VD):	0.261
Pgp-substrate:	68.44407653808594%

ADMET: Metabolism

CYP1A2-inhibitor:	0.006
CYP1A2-substrate:	0.933
CYP2C19-inhibitor:	0.018
CYP2C19-substrate:	0.32
CYP2C9-inhibitor:	0.012
CYP2C9-substrate:	0.057
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.12
CYP3A4-inhibitor:	0.008
CYP3A4-substrate:	0.18

ADMET: Excretion

Clearance (CL):	2.237
Half-life (T1/2):	0.672

ADMET: Toxicity

hERG Blockers:	0.013
Human Hepatotoxicity (H-HT):	0.053
Drug-inuced Liver Injury (DILI):	0.166
AMES Toxicity:	0.79
Rat Oral Acute Toxicity:	0.072
Maximum Recommended Daily Dose:	0.269
Skin Sensitization:	0.309
Carcinogencity:	0.025
Eye Corrosion:	0.005
Eye Irritation:	0.274
Respiratory Toxicity:	0.278

Download Data

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

Natural Product: NPC172373

Natural Product ID:	NPC172373
*Common Name:**	TXEJUZMIQVTZHO-FQUXZYTCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	TXEJUZMIQVTZHO-FQUXZYTCSA-N
Standard InCHI:	InChI=1S/C29H42O5/c1-15(17(3)27(33)34)7-8-16(2)19-9-10-20-25-23(31)13-21-18(4)22(30)11-12-28(21,5)26(25)24(32)14-29(19,20)6/h16-22,30H,1,7-14H2,2-6H3,(H,33,34)/t16-,17-,18+,19-,20+,21+,22-,28+,29-/m1/s1
SMILES:	C=C(CC[C@@H](C)[C@H]1CC[C@H]2C3=C(C(=O)C[C@]12C)[C@@]1(C)CC[C@H]([C@@H](C)[C@@H]1CC3=O)O)[C@@H](C)C(=O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001445] Bile acids, alcohols and derivatives [CHEMONTID:0002194] Hydroxy bile acids, alcohols and derivatives [CHEMONTID:0000260] Monohydroxy bile acids, alcohols 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
NPO14403	Taiwanofungus camphoratus	Species	Coriolaceae	Eukaryota	n.a.	fruit body	n.a.	PMID[15095145]
NPO14403	Taiwanofungus camphoratus	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17559265]
NPO14403	Taiwanofungus camphoratus	Species	Coriolaceae	Eukaryota	n.a.	mycelium	n.a.	PMID[17932820]
NPO14403	Taiwanofungus camphoratus	Species	Coriolaceae	Eukaryota	fruiting body	n.a.	n.a.	PMID[21028898]
NPO14403	Taiwanofungus camphoratus	Species	Coriolaceae	Eukaryota	n.a.	fruit body	n.a.	PMID[21028898]
NPO14403	Taiwanofungus camphoratus	Species	Coriolaceae	Eukaryota	fruiting body	n.a.	n.a.	PMID[21115251]
NPO14403	Taiwanofungus camphoratus	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23517145]
NPO14403	Taiwanofungus camphoratus	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31891260]
NPO14403	Taiwanofungus camphoratus	Species	Coriolaceae	Eukaryota	n.a.	fruit body	n.a.	PMID[8594142]
NPO15630	Manduca sexta	Species	Sphingidae	Eukaryota	n.a.	n.a.	n.a.	PMID[8748375]
NPO4176	Mosla scabra	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6926	Colubrina asiatica	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4176	Mosla scabra	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14403	Taiwanofungus camphoratus	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11787	Orthosiphon wulfenioides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6926	Colubrina asiatica	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17660	Podocarpus lawrencei	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25603	Lycoris x chejuensis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6926	Colubrina asiatica	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11557	Echinus miliaris	Species	Echinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27240	Alcyonium grandis	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29200	Moquiniastrum paniculatum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11787	Orthosiphon wulfenioides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15630	Manduca sexta	Species	Sphingidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4909	Hilliardiella oligocephala	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4176	Mosla scabra	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14403	Taiwanofungus camphoratus	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6533	Dipterocarpus pilosus	Species	Dipterocarpaceae	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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC172373 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	173
0.1-0.2	1178
0.2-0.3	4910
0.3-0.4	12001
0.4-0.5	9943
0.5-0.6	6354
0.6-0.7	5339
0.7-0.8	2350
0.8-0.85	247
0.85-0.9	147
0.9-0.95	48
0.95-1	7

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 NPC172373 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	152
0.1-0.2	1551
0.2-0.3	3931
0.3-0.4	2375
0.4-0.5	644
0.5-0.6	184
0.6-0.7	137
0.7-0.8	138
0.8-0.85	36
0.85-0.9	2
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