NPASS Compound

Structure

NPC482702 OpenBabel06302215502D 29 32 0 0 1 0 0 0 0 0999 V2000 -4.3301 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 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 -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 1 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 O 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 -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 -0.0000 2.0000 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 0.8660 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 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 3.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 2.3660 0.0000 C 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 -0.0000 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 -6.0622 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 29 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 14 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 28 1 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 9 14 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 15 1 6 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 15 26 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 18 25 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 19 26 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 24 1 0 0 0 0 22 25 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	392.2
Volume:	420.799
LogP:	6.976
LogD:	4.67
LogS:	-3.01
# Rotatable Bonds:	3
TPSA:	58.92
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.676
Synthetic Accessibility Score:	3.695
Fsp3:	0.36
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:	-4.907
MDCK Permeability:	2.3506794605054893e-05
Pgp-inhibitor:	0.997
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.023
20% Bioavailability (F20%):	0.275
30% Bioavailability (F30%):	0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.049
Plasma Protein Binding (PPB):	101.18373107910156%
Volume Distribution (VD):	2.982
Pgp-substrate:	1.5729619264602661%

ADMET: Metabolism

CYP1A2-inhibitor:	0.8
CYP1A2-substrate:	0.596
CYP2C19-inhibitor:	0.937
CYP2C19-substrate:	0.278
CYP2C9-inhibitor:	0.758
CYP2C9-substrate:	0.944
CYP2D6-inhibitor:	0.914
CYP2D6-substrate:	0.87
CYP3A4-inhibitor:	0.472
CYP3A4-substrate:	0.366

ADMET: Excretion

Clearance (CL):	8.233
Half-life (T1/2):	0.096

ADMET: Toxicity

hERG Blockers:	0.243
Human Hepatotoxicity (H-HT):	0.937
Drug-inuced Liver Injury (DILI):	0.055
AMES Toxicity:	0.053
Rat Oral Acute Toxicity:	0.672
Maximum Recommended Daily Dose:	0.952
Skin Sensitization:	0.936
Carcinogencity:	0.567
Eye Corrosion:	0.003
Eye Irritation:	0.432
Respiratory Toxicity:	0.845

Download Data

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

Natural Product: NPC482702

Natural Product ID:	NPC482702
*Common Name:**	PPYSNAHBRHGTLI-KRWDZBQOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PPYSNAHBRHGTLI-KRWDZBQOSA-N
Standard InCHI:	InChI=1S/C25H28O4/c1-15(2)5-7-19-21(26)9-6-16-13-17(14-28-24(16)19)18-8-10-22-20(23(18)27)11-12-25(3,4)29-22/h5-6,8-12,17,26-27H,7,13-14H2,1-4H3/t17-/m0/s1
SMILES:	CC(=CCc1c(ccc2C[C@@H](COc12)c1ccc2c(C=CC(C)(C)O2)c1O)O)C
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:0002506] Isoflavonoids [CHEMONTID:0003530] Pyranoisoflavonoids

*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
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[12713396]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	roots	n.a.	n.a.	PMID[20022509]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21866899]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23325115]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	Roots	n.a.	n.a.	PMID[23541646]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28140583]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7381508]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	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	9

Activity Type	# Activity
Cell Line	5
Individual Protein	3
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT178	Individual Protein	Protein-tyrosine phosphatase 1B	Homo sapiens	Inhibition	=	5.5	%	PMID[28140583]
NPT152	Individual Protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	FC	=	1.1	n.a.	PMID[28140583]
NPT113	Cell Line	RAW264.7	Mus musculus	Inhibition	=	3.6	%	PMID[28140583]
NPT65	Cell Line	HepG2	Homo sapiens	Inhibition	=	15.9	%	PMID[28140583]
NPT81	Cell Line	A549	Homo sapiens	Inhibition	=	10.2	%	PMID[28140583]
NPT83	Cell Line	MCF7	Homo sapiens	Inhibition	=	60.9	%	PMID[28140583]
NPT660	Cell Line	SW480	Homo sapiens	Inhibition	=	20.2	%	PMID[28140583]
NPT741	Individual Protein	Tyrosinase	Homo sapiens	Inhibition	=	12.9	%	PMID[28140583]
NPT2	Others	Unspecified		Inhibition	=	40.2	%	PMID[28140583]

☑ 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 NPC482702 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	393
0.1-0.2	1564
0.2-0.3	3929
0.3-0.4	12013
0.4-0.5	6578
0.5-0.6	4146
0.6-0.7	7688
0.7-0.8	5204
0.8-0.85	846
0.85-0.9	212
0.9-0.95	68
0.95-1	56

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 NPC482702 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	324
0.1-0.2	931
0.2-0.3	1565
0.3-0.4	2707
0.4-0.5	1780
0.5-0.6	1030
0.6-0.7	651
0.7-0.8	149
0.8-0.85	7
0.85-0.9	3
0.9-0.95	3
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