NPASS Compound

Structure

NPC146119 OpenBabel06302216022D 34 37 0 0 1 0 0 0 0 0999 V2000 1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 O 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 -0.8660 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 1 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 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 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 1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -5.5000 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 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 34 1 0 0 0 0 6 7 2 0 0 0 0 7 21 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 12 2 0 0 0 0 11 22 1 0 0 0 0 12 13 1 0 0 0 0 12 21 1 0 0 0 0 13 18 2 0 0 0 0 13 14 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 20 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 23 22 1 6 0 0 0 23 24 1 0 0 0 0 23 30 1 0 0 0 0 24 25 1 0 0 0 0 24 33 1 1 0 0 0 25 26 1 0 0 0 0 25 32 1 6 0 0 0 26 27 1 0 0 0 0 26 31 1 6 0 0 0 27 28 1 6 0 0 0 27 30 1 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	343.18
Volume:	359.146
LogP:	2.922
LogD:	3.164
LogS:	-2.944
# Rotatable Bonds:	3
TPSA:	51.16
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.928
Synthetic Accessibility Score:	2.654
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.802
MDCK Permeability:	1.4599857422581408e-05
Pgp-inhibitor:	0.244
Pgp-substrate:	0.584
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.842
30% Bioavailability (F30%):	0.3

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.984
Plasma Protein Binding (PPB):	71.74982452392578%
Volume Distribution (VD):	2.035
Pgp-substrate:	14.925037384033203%

ADMET: Metabolism

CYP1A2-inhibitor:	0.641
CYP1A2-substrate:	0.969
CYP2C19-inhibitor:	0.028
CYP2C19-substrate:	0.938
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.757
CYP2D6-inhibitor:	0.415
CYP2D6-substrate:	0.955
CYP3A4-inhibitor:	0.034
CYP3A4-substrate:	0.756

ADMET: Excretion

Clearance (CL):	11.118
Half-life (T1/2):	0.721

ADMET: Toxicity

hERG Blockers:	0.805
Human Hepatotoxicity (H-HT):	0.334
Drug-inuced Liver Injury (DILI):	0.871
AMES Toxicity:	0.234
Rat Oral Acute Toxicity:	0.261
Maximum Recommended Daily Dose:	0.821
Skin Sensitization:	0.71
Carcinogencity:	0.038
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.95

Download Data

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

Natural Product: NPC146119

Natural Product ID:	NPC146119
*Common Name:**	HJOBXPHWOUTSLV-VRUXIHJPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HJOBXPHWOUTSLV-VRUXIHJPSA-N
Standard InCHI:	InChI=1S/C22H22O12/c1-31-12-5-9(24)6-13-15(12)17(28)21(20(32-13)8-2-3-10(25)11(26)4-8)34-22-19(30)18(29)16(27)14(7-23)33-22/h2-6,14,16,18-19,22-27,29-30H,7H2,1H3/t14-,16+,18+,19-,22+/m0/s1
SMILES:	COc1cc(cc2c1c(=O)c(c(c1ccc(c(c1)O)O)o2)O[C@@H]1[C@H]([C@@H]([C@@H]([C@H](CO)O1)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003531] Flavonoid-3-O-glycosides

*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
NPO1775	Euphorbia pekinensis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18595	Ceratostigma plumbaginoides	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18595	Ceratostigma plumbaginoides	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1775	Euphorbia pekinensis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1775	Euphorbia pekinensis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1775	Euphorbia pekinensis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17221	Lagerstroemia parviflora	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9170	Pulsatilla pratensis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18528	Hyparrhenia hirta	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21784	Quillaja saponaria	Species	Quillajaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24158	Phyllanthus anisolobus	Species	Leiothrichidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17623	Melampodium linearilobum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15106	Agrostemma gracilis	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15774	Geranium pusillum	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19238	Choristoneura occidentalis	Species	Tortricidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18595	Ceratostigma plumbaginoides	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1775	Euphorbia pekinensis	Species	Euphorbiaceae	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 NPC146119 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	440
0.1-0.2	1822
0.2-0.3	4199
0.3-0.4	9805
0.4-0.5	8237
0.5-0.6	4214
0.6-0.7	5210
0.7-0.8	5295
0.8-0.85	1669
0.85-0.9	1102
0.9-0.95	496
0.95-1	208

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 NPC146119 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	404
0.1-0.2	944
0.2-0.3	1949
0.3-0.4	2684
0.4-0.5	1792
0.5-0.6	910
0.6-0.7	296
0.7-0.8	129
0.8-0.85	13
0.85-0.9	16
0.9-0.95	11
0.95-1	2

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