NPASS Compound

Structure

NPC162704 OpenBabel06302216202D 21 22 0 0 1 0 0 0 0 0999 V2000 2.0594 -2.2872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9254 -2.7872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6685 -2.1180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8765 -1.1399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4697 -0.2263 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.6037 0.2737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6092 0.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6581 -1.4781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0649 -2.3917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9309 -2.8917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3364 -1.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8364 -2.4487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7431 -0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7213 -0.4612 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0104 -0.6399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2129 0.4428 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1639 0.1338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3718 -0.8444 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9071 0.8029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 11 1 0 0 0 0 2 3 2 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 5 18 1 1 0 0 0 6 7 2 0 0 0 0 6 17 1 0 0 0 0 8 7 1 6 0 0 0 8 9 1 0 0 0 0 8 16 1 0 0 0 0 9 10 1 1 0 0 0 9 12 1 0 0 0 0 10 11 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 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 M END $$$$

Physi-Chem Properties

Molecular Weight:	638.37
Volume:	648.541
LogP:	2.257
LogD:	2.139
LogS:	-3.991
# Rotatable Bonds:	12
TPSA:	164.37
# H-Bond Aceptor:	11
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.166
Synthetic Accessibility Score:	5.819
Fsp3:	0.794
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.358
MDCK Permeability:	6.248988938750699e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.938
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.969

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.114
Plasma Protein Binding (PPB):	45.884124755859375%
Volume Distribution (VD):	0.828
Pgp-substrate:	28.436561584472656%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.082
CYP2C19-inhibitor:	0.005
CYP2C19-substrate:	0.434
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.017
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.051
CYP3A4-inhibitor:	0.345
CYP3A4-substrate:	0.264

ADMET: Excretion

Clearance (CL):	1.491
Half-life (T1/2):	0.295

ADMET: Toxicity

hERG Blockers:	0.043
Human Hepatotoxicity (H-HT):	0.223
Drug-inuced Liver Injury (DILI):	0.532
AMES Toxicity:	0.055
Rat Oral Acute Toxicity:	0.916
Maximum Recommended Daily Dose:	0.936
Skin Sensitization:	0.081
Carcinogencity:	0.922
Eye Corrosion:	0.003
Eye Irritation:	0.01
Respiratory Toxicity:	0.986

Download Data

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

Natural Product: NPC162704

Natural Product ID:	NPC162704
*Common Name:**	XENYZNVJFQEFDC-LFLWPQTJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XENYZNVJFQEFDC-LFLWPQTJSA-N
Standard InCHI:	InChI=1S/C17H22O4/c1-10-5-7-14-12(3)17(19)21-16(14)9-11(2)15(8-6-10)20-13(4)18/h6,9,14-16H,3,5,7-8H2,1-2,4H3/b10-6+,11-9+/t14-,15-,16+/m0/s1
SMILES:	C/C/1=CC[C@@H](/C(=C/[C@@H]2[C@@H](CC1)C(=C)C(=O)O2)/C)OC(=O)C
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:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001543] Sesquiterpene lactones [CHEMONTID:0001771] Germacranolides 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
NPO23451	Polytrichum commune	Species	Polytrichaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19572610]
NPO17263	Mimosa diplotricha	Species	Fabaceae	Eukaryota	whole plant	Taitung County, Taiwan	2009-MAY	PMID[21875046]
NPO17263	Mimosa diplotricha	Species	Fabaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[21875046]
NPO17263	Mimosa diplotricha	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27715048]
NPO23093	Blumea obliqua	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7494149]
NPO24213	Strophanthus thollonii	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23451	Polytrichum commune	Species	Polytrichaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18699	Baccharis articulata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23093	Blumea obliqua	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23687	Delphinium hybridum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24326	Adenocalymma alliaceum	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23451	Polytrichum commune	Species	Polytrichaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21955	Salvia deserta	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17263	Mimosa diplotricha	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22967	Maytenus blepharodes	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20909	Astragalus amarus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18436	Agave ghiesbreghtii	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21202	Galeopsis pubescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26367	Muriceopsis flavida	Species	Plexauridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24213	Strophanthus thollonii	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26758	Forsythia x intermedia	Species	Oleaceae	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 NPC162704 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	179
0.1-0.2	1350
0.2-0.3	6449
0.3-0.4	16362
0.4-0.5	9328
0.5-0.6	5951
0.6-0.7	2303
0.7-0.8	594
0.8-0.85	85
0.85-0.9	73
0.9-0.95	13
0.95-1	10

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 NPC162704 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	167
0.1-0.2	1907
0.2-0.3	4030
0.3-0.4	2120
0.4-0.5	640
0.5-0.6	227
0.6-0.7	48
0.7-0.8	11
0.8-0.85	0
0.85-0.9	0
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