NPASS Compound

Structure

CID236769 OpenBabel06191716032D 26 28 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 -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 -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 -2.5981 -1.5000 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 1.7321 -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 0.5000 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 -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 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 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 3.0000 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 3.4641 -0.0000 0.0000 O 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 -4.3301 0.5000 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 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 22 1 0 0 0 0 2 23 1 0 0 0 0 3 24 1 0 0 0 0 4 25 1 0 0 0 0 5 6 2 0 0 0 0 5 10 1 0 0 0 0 6 13 1 0 0 0 0 7 10 2 0 0 0 0 7 14 1 0 0 0 0 8 11 2 0 0 0 0 8 12 1 0 0 0 0 9 11 1 0 0 0 0 9 15 2 0 0 0 0 10 18 1 0 0 0 0 11 22 1 0 0 0 0 12 16 2 0 0 0 0 12 20 1 0 0 0 0 13 14 2 0 0 0 0 13 23 1 0 0 0 0 14 24 1 0 0 0 0 15 16 1 0 0 0 0 15 26 1 0 0 0 0 16 17 1 0 0 0 0 17 19 1 0 0 0 0 17 21 2 0 0 0 0 18 19 2 0 0 0 0 18 26 1 0 0 0 0 19 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	358.11
Volume:	351.951
LogP:	3.305
LogD:	2.906
LogS:	-4.397
# Rotatable Bonds:	5
TPSA:	87.36
# H-Bond Aceptor:	7
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.749
Synthetic Accessibility Score:	2.246
Fsp3:	0.211
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.704
MDCK Permeability:	3.5863384255208075e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.009

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.019
Plasma Protein Binding (PPB):	81.54876708984375%
Volume Distribution (VD):	0.86
Pgp-substrate:	17.187210083007812%

ADMET: Metabolism

CYP1A2-inhibitor:	0.873
CYP1A2-substrate:	0.974
CYP2C19-inhibitor:	0.744
CYP2C19-substrate:	0.601
CYP2C9-inhibitor:	0.699
CYP2C9-substrate:	0.925
CYP2D6-inhibitor:	0.381
CYP2D6-substrate:	0.926
CYP3A4-inhibitor:	0.756
CYP3A4-substrate:	0.427

ADMET: Excretion

Clearance (CL):	6.298
Half-life (T1/2):	0.662

ADMET: Toxicity

hERG Blockers:	0.034
Human Hepatotoxicity (H-HT):	0.161
Drug-inuced Liver Injury (DILI):	0.963
AMES Toxicity:	0.47
Rat Oral Acute Toxicity:	0.146
Maximum Recommended Daily Dose:	0.132
Skin Sensitization:	0.141
Carcinogencity:	0.034
Eye Corrosion:	0.004
Eye Irritation:	0.218
Respiratory Toxicity:	0.26

Download Data

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

Natural Product: NPC236769

Natural Product ID:	NPC236769
*Common Name:**	Retusin
IUPAC Name:	2-(3,4-dimethoxyphenyl)-5-hydroxy-3,7-dimethoxychromen-4-one
Synonyms:	NSC-61837
Standard InCHIKey:	HHGPYJLEJGNWJA-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C19H18O7/c1-22-11-8-12(20)16-15(9-11)26-18(19(25-4)17(16)21)10-5-6-13(23-2)14(7-10)24-3/h5-9,20H,1-4H3
SMILES:	COc1cc(c2c(c1)oc(c1ccc(c(c1)OC)OC)c(c2=O)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL77966
PubChem CID:	5352005
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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO28159	Rubia akane	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8176404]
NPO19745	Esox lucius	Species	Esocidae	Eukaryota	n.a.	n.a.	n.a.	PMID[3349210]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31291099]
NPO29463	Pogostemon cablin	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30188125]
NPO12796	Periploca sepium	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28294615]
NPO27600	Boesenbergia pandurata	Species	Zingiberaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[28099006]
NPO17376	Bacillus amyloliquefaciens	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[27934031]
NPO27600	Boesenbergia pandurata	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27508308]
NPO17376	Bacillus amyloliquefaciens	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24698790]
NPO17376	Bacillus amyloliquefaciens	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[23265519]

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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
ED50	2
GI50	49
IC50	41
Others	27

Activity Type	# Activity
Cell Line	78
CELL-LINE	1
Individual Protein	14
NON-MOLECULAR	15
Organism	3
Others	8

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		IC50	>	50000.0	nM	PMID[527475]
NPT762	Cell Line	A-431	Homo sapiens	IC50	=	82250.0	nM	PMID[527473]
NPT1719	Cell Line	2008	Homo sapiens	IC50	>	100000.0	nM	PMID[527473]
NPT762	Cell Line	A-431	Homo sapiens	Ratio IC50	=	1.4	n.a.	PMID[527473]
NPT71	Cell Line	HEK293	Homo sapiens	IC50	=	141870.0	nM	PMID[527473]
NPT71	Cell Line	HEK293	Homo sapiens	Ratio IC50	=	1.6	n.a.	PMID[527473]
NPT1083	Cell Line	A-375	Homo sapiens	IC50	=	69720.0	nM	PMID[527473]
NPT148	Cell Line	HCT-15	Homo sapiens	IC50	=	68110.0	nM	PMID[527473]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	100000.0	nM	PMID[527473]
NPT762	Cell Line	A-431	Homo sapiens	IC50	=	57540.0	nM	PMID[527473]

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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 NPC236769 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	426
0.1-0.2	1877
0.2-0.3	4806
0.3-0.4	10982
0.4-0.5	6530
0.5-0.6	3706
0.6-0.7	5092
0.7-0.8	4733
0.8-0.85	2267
0.85-0.9	1497
0.9-0.95	570
0.95-1	211

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Similarity Score	Similarity Level	Natural Product ID
0.9931	High Similarity	NPC166753
0.9931	High Similarity	NPC50728
0.9863	High Similarity	NPC236223
0.9863	High Similarity	NPC78326
0.9863	High Similarity	NPC179126

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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 NPC236769 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	398
0.1-0.2	985
0.2-0.3	1739
0.3-0.4	2645
0.4-0.5	1800
0.5-0.6	1021
0.6-0.7	375
0.7-0.8	126
0.8-0.85	36
0.85-0.9	16
0.9-0.95	8
0.95-1	1

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9463	High Similarity	NPD2801	Approved
0.94	High Similarity	NPD3817	Phase 2
0.9384	High Similarity	NPD1512	Approved
0.9338	High Similarity	NPD3882	Suspended
0.9267	High Similarity	NPD1934	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