NPASS Compound

Structure

NPC319108 OpenBabel06302216202D 32 35 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 -1.7321 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 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 -1.7321 -1.0000 0.0000 C 0 0 0 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 -0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 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 2.0000 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 -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 -3.4641 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 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 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 3 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 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 O 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 2.5981 -1.5000 0.0000 O 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 -2.5981 -5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 1 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 3 32 1 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 7 1 0 0 0 0 7 17 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 20 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 16 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 12 19 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 18 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 20 21 1 0 0 0 0 21 26 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 31 1 0 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 29 1 0 0 0 0 25 26 1 0 0 0 0 25 27 1 0 0 0 0 27 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	448.1
Volume:	413.147
LogP:	-0.02
LogD:	1.124
LogS:	-3.878
# Rotatable Bonds:	4
TPSA:	190.28
# H-Bond Aceptor:	11
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.279
Synthetic Accessibility Score:	3.884
Fsp3:	0.286
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
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:	-6.105
MDCK Permeability:	1.4388207091542426e-05
Pgp-inhibitor:	0.003
Pgp-substrate:	0.514
Human Intestinal Absorption (HIA):	0.627
20% Bioavailability (F20%):	0.23
30% Bioavailability (F30%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.074
Plasma Protein Binding (PPB):	87.82032012939453%
Volume Distribution (VD):	0.946
Pgp-substrate:	14.663725852966309%

ADMET: Metabolism

CYP1A2-inhibitor:	0.07
CYP1A2-substrate:	0.037
CYP2C19-inhibitor:	0.016
CYP2C19-substrate:	0.053
CYP2C9-inhibitor:	0.012
CYP2C9-substrate:	0.621
CYP2D6-inhibitor:	0.082
CYP2D6-substrate:	0.187
CYP3A4-inhibitor:	0.062
CYP3A4-substrate:	0.018

ADMET: Excretion

Clearance (CL):	3.554
Half-life (T1/2):	0.725

ADMET: Toxicity

hERG Blockers:	0.024
Human Hepatotoxicity (H-HT):	0.113
Drug-inuced Liver Injury (DILI):	0.979
AMES Toxicity:	0.775
Rat Oral Acute Toxicity:	0.111
Maximum Recommended Daily Dose:	0.011
Skin Sensitization:	0.057
Carcinogencity:	0.095
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.024

Download Data

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

Natural Product: NPC319108

Natural Product ID:	NPC319108
*Common Name:**	JPUKWEQWGBDDQB-LVIXBQNQSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JPUKWEQWGBDDQB-LVIXBQNQSA-N
Standard InCHI:	InChI=1S/C21H20O11/c22-7-13-15(26)17(28)18(29)21(31-13)32-20-16(27)14-11(25)5-10(24)6-12(14)30-19(20)8-1-3-9(23)4-2-8/h1-6,13,15,17-18,21-26,28-29H,7H2/t13?,15-,17?,18?,21-/m1/s1
SMILES:	C1=CC(=CC=C1C2=C(C(=O)C3=C(C=C(C=C3O2)O)O)OC4C(C(C(C(O4)CO)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44258798
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
NPO30570	Tetrapanax papyriferus	Species	Araliaceae	Eukaryota	n.a.	fruit	n.a.	PMID[16378372]
NPO30570	Tetrapanax papyriferus	Species	Araliaceae	Eukaryota	n.a.	flower	n.a.	PMID[16378372]
NPO17782	Inula britannica	Species	Asteraceae	Eukaryota	flowers	n.a.	n.a.	PMID[16643020]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19919095]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20815207]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[21319773]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	leaf	n.a.	PMID[21319773]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	bark	n.a.	PMID[21319773]
NPO18296	Diospyros kaki	Species	Ebenaceae	Eukaryota	n.a.	calyx	n.a.	PMID[21561086]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	leaf	n.a.	PMID[22207282]
NPO18007	Agrimonia pilosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22281186]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	flower buds and leaves	Khon Kaen province, Thailand	2010	PMID[23270663]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[23642481]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[23806866]
NPO18296	Diospyros kaki	Species	Ebenaceae	Eukaryota	n.a.	fruit	n.a.	PMID[24086493]
NPO18093	Rosa chinensis	Species	Rosaceae	Eukaryota	Flowers	Muyang, China	n.a.	PMID[24621197]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	root bark	University of Veterinary and Pharmaceutical Sciences Brno (UVPS Brno), Brno, Czech Republic	2011-APR	PMID[24901948]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	Konya, Turkey	2007-APR	PMID[24901948]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	leaves	Chungbuk, Korea	n.a.	PMID[25935644]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[25981820]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Flowers	n.a.	n.a.	PMID[26462418]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	latex	n.a.	PMID[27294120]
NPO18007	Agrimonia pilosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27588326]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	Root barks	n.a.	n.a.	PMID[3097265]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Rhizome	n.a.	n.a.	Database[FooDB]
NPO18007	Agrimonia pilosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30570	Tetrapanax papyriferus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29331	Pyrrosia sheareri	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18093	Rosa chinensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17782	Inula britannica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18296	Diospyros kaki	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1613	Cuscuta chinensis	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29331	Pyrrosia sheareri	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18093	Rosa chinensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1613	Cuscuta chinensis	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17782	Inula britannica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18007	Agrimonia pilosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18296	Diospyros kaki	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18007	Agrimonia pilosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29331	Pyrrosia sheareri	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30570	Tetrapanax papyriferus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17782	Inula britannica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18093	Rosa chinensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1613	Cuscuta chinensis	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18296	Diospyros kaki	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18296	Diospyros kaki	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17782	Inula britannica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29331	Pyrrosia sheareri	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18007	Agrimonia pilosa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1613	Cuscuta chinensis	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18093	Rosa chinensis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18296	Diospyros kaki	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17782	Inula britannica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29331	Pyrrosia sheareri	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18007	Agrimonia pilosa	Species	Rosaceae	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 NPC319108 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 NPC319108 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