NPASS Compound

Structure

NPC291149 OpenBabel06302215432D 29 32 0 0 1 0 0 0 0 0999 V2000 -1.5904 -5.6846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0781 -4.8405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5909 -3.9961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6160 -3.9958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1288 -3.1514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8461 -3.1511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3333 -2.3067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3081 -2.3064 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8456 -1.4626 0.0000 O 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 2 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 -2.5362 2.4384 0.0000 C 0 0 0 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 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 -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 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 2 0 0 0 0 7 9 1 0 0 0 0 10 9 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 15 1 1 0 0 0 14 25 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 23 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 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:	400.3
Volume:	442.488
LogP:	6.192
LogD:	4.695
LogS:	-5.671
# Rotatable Bonds:	7
TPSA:	43.37
# H-Bond Aceptor:	3
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.294
Synthetic Accessibility Score:	4.068
Fsp3:	0.846
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.718
MDCK Permeability:	1.711650656943675e-05
Pgp-inhibitor:	0.906
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.993
30% Bioavailability (F30%):	0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.769
Plasma Protein Binding (PPB):	94.53180694580078%
Volume Distribution (VD):	0.657
Pgp-substrate:	1.4648653268814087%

ADMET: Metabolism

CYP1A2-inhibitor:	0.229
CYP1A2-substrate:	0.138
CYP2C19-inhibitor:	0.259
CYP2C19-substrate:	0.57
CYP2C9-inhibitor:	0.454
CYP2C9-substrate:	0.431
CYP2D6-inhibitor:	0.032
CYP2D6-substrate:	0.167
CYP3A4-inhibitor:	0.89
CYP3A4-substrate:	0.317

ADMET: Excretion

Clearance (CL):	11.283
Half-life (T1/2):	0.586

ADMET: Toxicity

hERG Blockers:	0.931
Human Hepatotoxicity (H-HT):	0.091
Drug-inuced Liver Injury (DILI):	0.839
AMES Toxicity:	0.021
Rat Oral Acute Toxicity:	0.04
Maximum Recommended Daily Dose:	0.818
Skin Sensitization:	0.961
Carcinogencity:	0.478
Eye Corrosion:	0.809
Eye Irritation:	0.241
Respiratory Toxicity:	0.958

Download Data

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

Natural Product: NPC291149

Natural Product ID:	NPC291149
*Common Name:**	VOCBWIIFXDYGNZ-IXKNJLPQSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VOCBWIIFXDYGNZ-IXKNJLPQSA-N
Standard InCHI:	InChI=1S/C26H40O3/c1-4-5-6-7-8-24(28)29-23-12-11-21-20-10-9-18-17-19(27)13-15-25(18,2)22(20)14-16-26(21,23)3/h17,20-23H,4-16H2,1-3H3/t20-,21-,22-,23-,25-,26-/m0/s1
SMILES:	CCCCCCC(=O)O[C@H]1CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	9416
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001691] Steroid esters

*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
NPO26327	Chaenomeles sinensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14600382]
NPO26327	Chaenomeles sinensis	Species	Rosaceae	Eukaryota	Twigs	n.a.	n.a.	PMID[25894905]
NPO26327	Chaenomeles sinensis	Species	Rosaceae	Eukaryota	Twigs	n.a.	n.a.	PMID[28358502]
NPO21620	Thlaspi arvense	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7642	Cleome gynandra	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26327	Chaenomeles sinensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7642	Cleome gynandra	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26327	Chaenomeles sinensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21620	Thlaspi arvense	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21620	Thlaspi arvense	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26327	Chaenomeles sinensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21620	Thlaspi arvense	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26327	Chaenomeles sinensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7642	Cleome gynandra	Species	Cleomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21620	Thlaspi arvense	Species	Brassicaceae	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	13

Activity Type	# Activity
ORGANISM	1
PHENOTYPE	12

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20596	PHENOTYPE	Hepatotoxicity	n.a.	Composite Activity - Active	=	0.0	n.a.	PMID[515004]
NPT20596	PHENOTYPE	Hepatotoxicity	n.a.	Composite Activity - Marginal	=	0.0	n.a.	PMID[515004]
NPT20596	PHENOTYPE	Hepatotoxicity	n.a.	Alkaline Phosphatase Increase - Index Value	=	0.0	n.a.	PMID[515004]
NPT20596	PHENOTYPE	Hepatotoxicity	n.a.	Alkaline Phosphatase Increase - Number of Reports	<	4.0	n.a.	PMID[515004]
NPT20596	PHENOTYPE	Hepatotoxicity	n.a.	SGOT Increase - Number of Reports	<	4.0	n.a.	PMID[515004]
NPT20596	PHENOTYPE	Hepatotoxicity	n.a.	SGOT Increase - Index Value	=	4.8	n.a.	PMID[515004]
NPT20596	PHENOTYPE	Hepatotoxicity	n.a.	SGPT Increase - Number of Reports	<	4.0	n.a.	PMID[515004]
NPT20596	PHENOTYPE	Hepatotoxicity	n.a.	SGPT Increase - Index Value	=	7.2	n.a.	PMID[515004]
NPT20596	PHENOTYPE	Hepatotoxicity	n.a.	LDH Increase - Index Value	=	2.4	n.a.	PMID[515004]
NPT20596	PHENOTYPE	Hepatotoxicity	n.a.	LDH Increase - Number of Reports	<	4.0	n.a.	PMID[515004]
NPT20596	PHENOTYPE	Hepatotoxicity	n.a.	GGT Increase - Number of Reports	<	4.0	n.a.	PMID[515004]
NPT20596	PHENOTYPE	Hepatotoxicity	n.a.	GGT Increase - Index Value	=	4.8	n.a.	PMID[515004]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Hit score	=	0.1237	n.a.	PMID[515005]

☑ 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 NPC291149 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 NPC291149 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