NPASS Compound

Structure

CID253662 OpenBabel06191716052D 33 36 0 0 1 0 0 0 0 0999 V2000 -3.4641 -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 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 4.0000 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 1.7321 0.0000 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 -0.8660 4.5000 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 -5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 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 -0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 2 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 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 -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 -0.8660 -0.5000 0.0000 C 0 0 2 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 -0.8660 5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -0.5000 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 0.8660 2.5000 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 1.0000 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 -1.7321 -2.0000 0.0000 O 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 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 1 7 1 0 0 0 0 2 9 1 0 0 0 0 3 7 2 0 0 0 0 3 10 1 0 0 0 0 4 8 2 0 0 0 0 4 11 1 0 0 0 0 5 8 1 0 0 0 0 5 12 2 0 0 0 0 6 22 1 0 0 0 0 7 19 1 0 0 0 0 8 23 1 0 0 0 0 9 10 2 0 0 0 0 9 24 1 0 0 0 0 10 25 1 0 0 0 0 11 14 2 0 0 0 0 11 26 1 0 0 0 0 12 14 1 0 0 0 0 12 31 1 0 0 0 0 13 6 1 6 0 0 0 13 15 1 0 0 0 0 13 32 1 0 0 0 0 14 16 1 0 0 0 0 15 17 1 0 0 0 0 15 27 1 1 0 0 0 16 20 1 0 0 0 0 16 28 2 0 0 0 0 17 18 1 0 0 0 0 17 29 1 6 0 0 0 18 21 1 0 0 0 0 18 30 1 1 0 0 0 19 20 2 0 0 0 0 19 31 1 0 0 0 0 20 33 1 0 0 0 0 21 32 1 0 0 0 0 21 33 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	464.1
Volume:	421.937
LogP:	0.264
LogD:	-0.013
LogS:	-3.564
# Rotatable Bonds:	4
TPSA:	210.51
# H-Bond Aceptor:	12
# H-Bond Donor:	8
# Rings:	4
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.229
Synthetic Accessibility Score:	4.008
Fsp3:	0.286
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.265
MDCK Permeability:	6.821358510933351e-06
Pgp-inhibitor:	0.006
Pgp-substrate:	0.432
Human Intestinal Absorption (HIA):	0.733
20% Bioavailability (F20%):	0.86
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.016
Plasma Protein Binding (PPB):	89.1961898803711%
Volume Distribution (VD):	0.845
Pgp-substrate:	13.478715896606445%

ADMET: Metabolism

CYP1A2-inhibitor:	0.325
CYP1A2-substrate:	0.038
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.045
CYP2C9-inhibitor:	0.073
CYP2C9-substrate:	0.252
CYP2D6-inhibitor:	0.165
CYP2D6-substrate:	0.164
CYP3A4-inhibitor:	0.104
CYP3A4-substrate:	0.011

ADMET: Excretion

Clearance (CL):	6.828
Half-life (T1/2):	0.914

ADMET: Toxicity

hERG Blockers:	0.126
Human Hepatotoxicity (H-HT):	0.172
Drug-inuced Liver Injury (DILI):	0.979
AMES Toxicity:	0.832
Rat Oral Acute Toxicity:	0.042
Maximum Recommended Daily Dose:	0.009
Skin Sensitization:	0.829
Carcinogencity:	0.051
Eye Corrosion:	0.003
Eye Irritation:	0.756
Respiratory Toxicity:	0.022

Download Data

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

Natural Product: NPC253662

Natural Product ID:	NPC253662
*Common Name:**	Miquelianin
IUPAC Name:	2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxychromen-4-one
Synonyms:	Miquelianin
Standard InCHIKey:	OVSQVDMCBVZWGM-DHALZPNHSA-N
Standard InCHI:	InChI=1S/C21H20O12/c22-6-13-15(27)17(29)18(30)21(32-13)33-20-16(28)14-11(26)4-8(23)5-12(14)31-19(20)7-1-2-9(24)10(25)3-7/h1-5,13,15,17-18,21-27,29-30H,6H2/t13-,15-,17+,18-,21-/m1/s1
SMILES:	OC[C@H]1O[C@H](Oc2c(oc3c(c2=O)c(O)cc(c3)O)c2ccc(c(c2)O)O)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1098724
PubChem CID:	12304323
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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO7381	Ircinia spinosula	Species	Irciniidae	Eukaryota	n.a.	Bay of Naples, Italy	n.a.	PMID[7714539]
NPO26927	Salacia madagascariensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7288445]
NPO20150	Erythrina sacleuxii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33170684]
NPO10300	Tropaeolum majus	Species	Tropaeolaceae	Eukaryota	Flowers	São Paulo, Brazil.		PMID[32156350]
NPO14827	Rhus chinensis	Species	Anacardiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[32031812]
NPO26451	Ophiocoma scolopendrina	Species	Ophiocomidae	Eukaryota	n.a.	n.a.	n.a.	PMID[27684202]
NPO25769	Heterotheca inuloides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26566007]
NPO25887	Turbinaria ornata	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2607351]
NPO25887	Turbinaria ornata	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25050371]
NPO25197	Magnolia sprengeri	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22080044]

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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	1
Ki	1
Others	4

Activity Type	# Activity
Cell Line	1
Individual Protein	4
Organism	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT71	Cell Line	HEK293	Homo sapiens	Inhibition	=	-1.86	%	PMID[529382]
NPT1606	Individual Protein	NADPH oxidase 4	Homo sapiens	IC50	=	830.0	nM	PMID[529382]
NPT1606	Individual Protein	NADPH oxidase 4	Homo sapiens	Inhibition	=	105.0	%	PMID[529382]
NPT1606	Individual Protein	NADPH oxidase 4	Homo sapiens	Inhibition	=	104.63	%	PMID[529382]
NPT224	Individual Protein	Alpha-2c adrenergic receptor	Homo sapiens	Ki	=	4063.0	nM	PMID[529381]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	TIME	=	0.02483	hr	PMID[529381]

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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 NPC253662 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	463
0.1-0.2	1895
0.2-0.3	4423
0.3-0.4	10023
0.4-0.5	7901
0.5-0.6	4220
0.6-0.7	5307
0.7-0.8	5185
0.8-0.85	1550
0.85-0.9	1099
0.9-0.95	438
0.95-1	193

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC179950
1.0	High Similarity	NPC88789
1.0	High Similarity	NPC145038
1.0	High Similarity	NPC281131
1.0	High Similarity	NPC274618

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 NPC253662 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	421
0.1-0.2	956
0.2-0.3	2010
0.3-0.4	2681
0.4-0.5	1740
0.5-0.6	889
0.6-0.7	294
0.7-0.8	122
0.8-0.85	9
0.85-0.9	17
0.9-0.95	10
0.95-1	1

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.975	High Similarity	NPD6797	Phase 2
0.9689	High Similarity	NPD7251	Discontinued
0.963	High Similarity	NPD4338	Clinical (unspecified phase)
0.9509	High Similarity	NPD7808	Phase 3
0.9503	High Similarity	NPD7054	Approved

Showing 1 to 5 of 200 entries

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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