NPASS Compound

Structure

CID179126 OpenBabel06191715552D 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 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.5000 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 -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 -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 1.7321 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 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 -4.3301 -1.5000 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 0.5000 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 -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 12 1 0 0 0 0 7 10 2 0 0 0 0 7 13 1 0 0 0 0 8 11 2 0 0 0 0 8 14 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 13 2 0 0 0 0 12 20 1 0 0 0 0 13 23 1 0 0 0 0 14 16 2 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:	3.212
LogD:	2.881
LogS:	-4.461
# 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:	2.308
Fsp3:	0.211
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.69
MDCK Permeability:	3.5308534279465675e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.026
Plasma Protein Binding (PPB):	80.21288299560547%
Volume Distribution (VD):	0.859
Pgp-substrate:	19.85715675354004%

ADMET: Metabolism

CYP1A2-inhibitor:	0.868
CYP1A2-substrate:	0.974
CYP2C19-inhibitor:	0.729
CYP2C19-substrate:	0.479
CYP2C9-inhibitor:	0.723
CYP2C9-substrate:	0.924
CYP2D6-inhibitor:	0.348
CYP2D6-substrate:	0.929
CYP3A4-inhibitor:	0.755
CYP3A4-substrate:	0.363

ADMET: Excretion

Clearance (CL):	6.328
Half-life (T1/2):	0.75

ADMET: Toxicity

hERG Blockers:	0.027
Human Hepatotoxicity (H-HT):	0.158
Drug-inuced Liver Injury (DILI):	0.96
AMES Toxicity:	0.486
Rat Oral Acute Toxicity:	0.136
Maximum Recommended Daily Dose:	0.097
Skin Sensitization:	0.102
Carcinogencity:	0.036
Eye Corrosion:	0.004
Eye Irritation:	0.675
Respiratory Toxicity:	0.257

Download Data

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

Natural Product: NPC179126

Natural Product ID:	NPC179126
*Common Name:**	2-(4-Hydroxy-3-Methoxyphenyl)-3,5,7-Trimethoxychromen-4-One
IUPAC Name:	2-(4-hydroxy-3-methoxyphenyl)-3,5,7-trimethoxychromen-4-one
Synonyms:
Standard InCHIKey:	KOCIOXYNAFGQMZ-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C19H18O7/c1-22-11-8-14(24-3)16-15(9-11)26-18(19(25-4)17(16)21)10-5-6-12(20)13(7-10)23-2/h5-9,20H,1-4H3
SMILES:	COc1cc(c2c(c1)oc(c1ccc(c(c1)OC)O)c(c2=O)OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL361803
PubChem CID:	13942543
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
NPO40203	Miliusa cuneata	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26928423]
NPO33252	heliotropium sinuatum	Species	Heliotropiaceae	Eukaryota	resinous exudate	n.a.	n.a.	PMID[15603945]
NPO28468	Aglaia duperreana	Species	Meliaceae	Eukaryota	n.a.	root	n.a.	DOI[10.1021/np990242g]
NPO28536	Dictyostelium discoideum	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12203	Uvaria dulcis	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28468	Aglaia duperreana	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25238	Rheum coreanum	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26376	Camptorrhiza strumosa	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25523	Ageratina ixiocladon	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25985	Dryas octopetala	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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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	4
Others	1

Activity Type	# Activity
Cell Line	2
Organism	2
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT91	Cell Line	KB	Homo sapiens	IC50	>	47800.0	nM	PMID[458778]
NPT189	Cell Line	Vero	Chlorocebus aethiops	IC50	>	47800.0	nM	PMID[458778]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	31500.0	nM	PMID[458778]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	27900.0	nM	PMID[458778]
NPT610	Others	Molecular identity unknown		Ratio	=	125.0	n.a.	PMID[458777]

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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 NPC179126 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	438
0.1-0.2	1888
0.2-0.3	4892
0.3-0.4	11047
0.4-0.5	6412
0.5-0.6	3763
0.6-0.7	5064
0.7-0.8	4768
0.8-0.85	2120
0.85-0.9	1345
0.9-0.95	691
0.95-1	269

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC236223
1.0	High Similarity	NPC78326
1.0	High Similarity	NPC270620
0.9932	High Similarity	NPC82325
0.9932	High Similarity	NPC279989

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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 NPC179126 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	402
0.1-0.2	973
0.2-0.3	1807
0.3-0.4	2643
0.4-0.5	1781
0.5-0.6	990
0.6-0.7	385
0.7-0.8	110
0.8-0.85	31
0.85-0.9	16
0.9-0.95	7
0.95-1	5

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9597	High Similarity	NPD2801	Approved
0.9521	High Similarity	NPD1512	Approved
0.947	High Similarity	NPD3882	Suspended
0.9404	High Similarity	NPD3817	Phase 2
0.94	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