NPASS Compound

Structure

NPC53078 OpenBabel06302216002D 28 30 0 0 0 0 0 0 0 0999 V2000 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 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 -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 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 -1.7321 -2.0000 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 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 0.0000 C 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 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 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 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 3.4641 -0.0000 0.0000 C 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 4.3301 -0.5000 0.0000 O 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 1.5000 0.0000 O 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 2.5981 2.5000 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 2.5981 -1.5000 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 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 26 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 11 1 0 0 0 0 7 8 1 0 0 0 0 7 10 1 0 0 0 0 8 9 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 14 2 0 0 0 0 13 27 1 0 0 0 0 14 15 1 0 0 0 0 14 26 1 0 0 0 0 15 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 17 25 1 0 0 0 0 18 19 2 0 0 0 0 18 23 1 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 27 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	390.1
Volume:	369.531
LogP:	2.531
LogD:	2.238
LogS:	-3.875
# Rotatable Bonds:	5
TPSA:	127.82
# H-Bond Aceptor:	9
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.563
Synthetic Accessibility Score:	2.654
Fsp3:	0.211
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.033
MDCK Permeability:	1.9925857486668974e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.057
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003
Plasma Protein Binding (PPB):	84.69023895263672%
Volume Distribution (VD):	0.858
Pgp-substrate:	27.363622665405273%

ADMET: Metabolism

CYP1A2-inhibitor:	0.445
CYP1A2-substrate:	0.979
CYP2C19-inhibitor:	0.045
CYP2C19-substrate:	0.185
CYP2C9-inhibitor:	0.585
CYP2C9-substrate:	0.646
CYP2D6-inhibitor:	0.044
CYP2D6-substrate:	0.37
CYP3A4-inhibitor:	0.339
CYP3A4-substrate:	0.26

ADMET: Excretion

Clearance (CL):	4.781
Half-life (T1/2):	0.877

ADMET: Toxicity

hERG Blockers:	0.153
Human Hepatotoxicity (H-HT):	0.085
Drug-inuced Liver Injury (DILI):	0.962
AMES Toxicity:	0.254
Rat Oral Acute Toxicity:	0.203
Maximum Recommended Daily Dose:	0.126
Skin Sensitization:	0.778
Carcinogencity:	0.019
Eye Corrosion:	0.003
Eye Irritation:	0.857
Respiratory Toxicity:	0.159

Download Data

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

Natural Product: NPC53078

Natural Product ID:	NPC53078
*Common Name:**	DTODSGVQMWBBNE-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DTODSGVQMWBBNE-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C19H18O9/c1-24-11-7-10-13(15(22)14(11)21)16(23)19(27-4)17(28-10)8-5-9(20)18(26-3)12(6-8)25-2/h5-7,20-22H,1-4H3
SMILES:	COc1cc2c(c(c1O)O)c(=O)c(c(c1cc(c(c(c1)OC)OC)O)o2)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	4277185
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002585] O-methylated flavonoids [CHEMONTID:0002592] 7-O-methylated flavonoids

*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
NPO22842	Lissoclinum bistratum	Species	Didemnidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12608858]
NPO23263	Crinum yemense	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15270564]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	flowers	n.a.	n.a.	PMID[16180811]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22014228]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	branch	n.a.	PMID[22014228]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22014228]
NPO22842	Lissoclinum bistratum	Species	Didemnidae	Eukaryota	n.a.	n.a.	n.a.	PMID[7807120]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Oil	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Sprout Seedling	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Flower	n.a.	n.a.	Database[FooDB]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO22186	Baileya pauciradiata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23107	Adiantum monochlamys	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22186	Baileya pauciradiata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22186	Baileya pauciradiata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23510	Vicia faba	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23648	Spilanthes mauritiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23427	Becium grandiflorum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO22842	Lissoclinum bistratum	Species	Didemnidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22186	Baileya pauciradiata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18884	Apuleia leiocarpa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13731	Centaurea webbiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6943	Vernonanthura chamaedrys	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20857	Commiphora erythraea	Species	Burseraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23107	Adiantum monochlamys	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23562	Pachyphragma macrophyllum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23263	Crinum yemense	Species	Amaryllidaceae	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 NPC53078 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	446
0.1-0.2	1989
0.2-0.3	5134
0.3-0.4	11242
0.4-0.5	6100
0.5-0.6	3997
0.6-0.7	5099
0.7-0.8	4807
0.8-0.85	1914
0.85-0.9	1098
0.9-0.95	653
0.95-1	218

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 NPC53078 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	415
0.1-0.2	1001
0.2-0.3	1970
0.3-0.4	2676
0.4-0.5	1676
0.5-0.6	947
0.6-0.7	309
0.7-0.8	107
0.8-0.85	26
0.85-0.9	15
0.9-0.95	7
0.95-1	1

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