NPASS Compound

Structure

CID259767 OpenBabel06191716062D 30 32 0 0 1 0 0 0 0 0999 V2000 2.5981 -0.5000 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 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 0.0000 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 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -0.5000 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 7.7942 -1.5000 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 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -0.5000 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 6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 2 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 8.6603 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -3.0000 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 0.8660 1.5000 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 5 1 0 0 0 0 1 11 2 0 0 0 0 2 6 2 0 0 0 0 2 11 1 0 0 0 0 3 8 2 0 0 0 0 3 11 1 0 0 0 0 4 7 2 0 0 0 0 4 12 1 0 0 0 0 5 13 2 0 0 0 0 6 13 1 0 0 0 0 7 14 1 0 0 0 0 8 15 1 0 0 0 0 9 12 2 0 0 0 0 9 16 1 0 0 0 0 10 22 1 0 0 0 0 12 23 1 0 0 0 0 13 29 1 0 0 0 0 14 15 1 0 0 0 0 14 16 2 0 0 0 0 15 24 2 0 0 0 0 16 25 1 0 0 0 0 17 10 1 6 0 0 0 17 18 1 0 0 0 0 17 30 1 0 0 0 0 18 19 1 0 0 0 0 18 26 1 1 0 0 0 19 20 1 0 0 0 0 19 27 1 6 0 0 0 20 21 1 0 0 0 0 20 28 1 1 0 0 0 21 29 1 6 0 0 0 21 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	418.13
Volume:	404.123
LogP:	1.24
LogD:	0.774
LogS:	-4.13
# Rotatable Bonds:	6
TPSA:	156.91
# H-Bond Aceptor:	9
# H-Bond Donor:	6
# Rings:	3
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.284
Synthetic Accessibility Score:	3.647
Fsp3:	0.286
Lipinski Rule-of-5:	Accepted
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:	-5.741
MDCK Permeability:	6.582420155609725e-06
Pgp-inhibitor:	0.002
Pgp-substrate:	0.02
Human Intestinal Absorption (HIA):	0.454
20% Bioavailability (F20%):	0.212
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.173
Plasma Protein Binding (PPB):	96.32495880126953%
Volume Distribution (VD):	0.692
Pgp-substrate:	1.6396890878677368%

ADMET: Metabolism

CYP1A2-inhibitor:	0.512
CYP1A2-substrate:	0.026
CYP2C19-inhibitor:	0.078
CYP2C19-substrate:	0.054
CYP2C9-inhibitor:	0.041
CYP2C9-substrate:	0.808
CYP2D6-inhibitor:	0.472
CYP2D6-substrate:	0.338
CYP3A4-inhibitor:	0.652
CYP3A4-substrate:	0.061

ADMET: Excretion

Clearance (CL):	6.134
Half-life (T1/2):	0.69

ADMET: Toxicity

hERG Blockers:	0.275
Human Hepatotoxicity (H-HT):	0.026
Drug-inuced Liver Injury (DILI):	0.582
AMES Toxicity:	0.719
Rat Oral Acute Toxicity:	0.211
Maximum Recommended Daily Dose:	0.006
Skin Sensitization:	0.918
Carcinogencity:	0.871
Eye Corrosion:	0.003
Eye Irritation:	0.683
Respiratory Toxicity:	0.035

Download Data

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

Natural Product: NPC259767

Natural Product ID:	NPC259767
*Common Name:**	Isoliquiritin
IUPAC Name:	(E)-1-(2,4-dihydroxyphenyl)-3-[4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenyl]prop-2-en-1-one
Synonyms:	Isoliquiritin
Standard InCHIKey:	YNWXJFQOCHMPCK-LXGDFETPSA-N
Standard InCHI:	InChI=1S/C21H22O9/c22-10-17-18(26)19(27)20(28)21(30-17)29-13-5-1-11(2-6-13)3-8-15(24)14-7-4-12(23)9-16(14)25/h1-9,17-23,25-28H,10H2/b8-3+/t17-,18-,19+,20-,21-/m1/s1
SMILES:	c1cc(ccc1/C=C/C(=O)c1ccc(cc1O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL599763
PubChem CID:	5318591
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid 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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7381508]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	Along the Valencian coast, Spain	2020-Jun&Jul	PMID[35161358]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32196343]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31625751]
NPO1698	Glycyrrhiza inflata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29641206]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29517238]
NPO1698	Glycyrrhiza inflata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28522265]
NPO29384	Glycyrrhiza glabra	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28140583]
NPO26395	Siegesbeckia pubescens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28009521]
NPO7154	Glycyrrhiza uralensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26841168]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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
IC50	3
Ki	1
Others	1

Activity Type	# Activity
Individual Protein	3
Others	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1592	Individual Protein	Dipeptidyl peptidase IV	Homo sapiens	IC50	=	26920.0	nM	PMID[514311]
NPT178	Individual Protein	Protein-tyrosine phosphatase 1B	Homo sapiens	Inhibition	<	50.0	%	PMID[514310]
NPT41	Individual Protein	Aldose reductase	Homo sapiens	IC50	=	720.0	nM	PMID[514309]
NPT2	Others	Unspecified	""	IC50	=	124000.0	nM	PMID[514308]
NPT2	Others	Unspecified	""	Ki	=	94000.0	nM	PMID[514308]

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☑ 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 NPC259767 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	379
0.1-0.2	1521
0.2-0.3	3734
0.3-0.4	9022
0.4-0.5	9361
0.5-0.6	4194
0.6-0.7	5361
0.7-0.8	5713
0.8-0.85	2319
0.85-0.9	918
0.9-0.95	143
0.95-1	32

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC88484
0.9864	High Similarity	NPC99233
0.9863	High Similarity	NPC121001
0.9863	High Similarity	NPC259182
0.9797	High Similarity	NPC265480

Showing 1 to 5 of 200 entries

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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 NPC259767 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	330
0.1-0.2	855
0.2-0.3	1752
0.3-0.4	2678
0.4-0.5	1905
0.5-0.6	1076
0.6-0.7	353
0.7-0.8	152
0.8-0.85	35
0.85-0.9	13
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9732	High Similarity	NPD4381	Clinical (unspecified phase)
0.9114	High Similarity	NPD3818	Discontinued
0.9073	High Similarity	NPD4380	Phase 2
0.9057	High Similarity	NPD7804	Clinical (unspecified phase)
0.9057	High Similarity	NPD7054	Approved

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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