NPASS Compound

Natural Product: NPC469758

Natural Product ID	NPC469758
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	4',7-Di-O-Methyl Naringenin
IUPAC Name	(2S)-7-acetyl-5-hydroxy-2-(4-methoxyphenyl)-2,3-dihydrochromen-4-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1169910
PubChem CID	49797761
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002585] O-methylated flavonoids [CHEMONTID:0002596] 4'-O-methylated flavonoids

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 39 41 0 0 0 0 0 0 0 0999 V2000 5.4001 2.4616 0.0942 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1107 2.2889 -0.6152 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7356 3.1975 -1.3918 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3051 1.1067 -0.4191 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7533 0.1119 0.4547 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9880 -1.0215 0.6470 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7705 -1.1771 -0.0268 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9481 -2.3602 0.1589 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1489 -3.1023 1.1270 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1413 -2.6681 -0.8326 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7547 -1.4399 -1.3907 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1372 -0.3630 -1.5391 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3212 -0.2065 -0.8869 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1016 0.9195 -1.0654 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9247 -0.9181 -0.6471 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5355 -1.5348 0.4121 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6245 -0.9930 1.0600 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1539 0.2123 0.6632 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5522 0.8460 -0.3998 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4515 0.2905 -1.0488 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2551 0.7432 1.3311 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7689 1.9866 0.8904 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3936 -2.0294 1.5018 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1122 1.7108 -0.3439 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7898 3.4876 0.0213 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3094 2.1465 1.1750 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6745 0.2189 0.9709 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3968 -3.2259 -1.6569 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8396 -3.4140 -0.4155 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1304 -1.6736 -2.4273 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7211 1.6695 -1.7509 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1681 -2.4648 0.7598 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0753 -1.5190 1.8951 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9384 1.7940 -0.7413 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9864 0.7957 -1.8821 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8959 2.0355 -0.2076 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0818 2.8085 1.2230 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7635 2.1018 1.4063 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9240 -2.8219 1.1536 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 2 0 11 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 18 21 1 0 21 22 1 0 6 23 1 0 14 4 1 0 13 7 1 0 20 15 1 0 1 24 1 0 1 25 1 0 1 26 1 0 5 27 1 0 10 28 1 0 10 29 1 0 11 30 1 0 14 31 1 0 16 32 1 0 17 33 1 0 19 34 1 0 20 35 1 0 22 36 1 0 22 37 1 0 22 38 1 0 23 39 1 0 M END

Standard InCHIKey	KHXZCJPKCAEZQD-INIZCTEOSA-N
Standard InCHI	InChI=1S/C18H16O5/c1-10(19)12-7-14(20)18-15(21)9-16(23-17(18)8-12)11-3-5-13(22-2)6-4-11/h3-8,16,20H,9H2,1-2H3/t16-/m0/s1
SMILES	CC(=O)C1=CC(=C2C(=O)CC(OC2=C1)C3=CC=C(C=C3)OC)O

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO23852	Cryptocarya obovata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15165150]
NPO23852	Cryptocarya obovata	Species	Lauraceae	Eukaryota	n.a.	trunk bark	n.a.	PMID[15165150]
NPO23852	Cryptocarya obovata	Species	Lauraceae	Eukaryota	n.a.	fruit	n.a.	PMID[15165150]
NPO23852	Cryptocarya obovata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20558060]
NPO23852	Cryptocarya obovata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO23852	Cryptocarya obovata	Species	Lauraceae	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	Organism Name	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
IC50	1
Inhibition	1

Activity Type	# Activity
Cell line	1
Organism	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT71	Cell line	HEK293	Homo sapiens	IC50	>	83000.0	nM	PMID[19581457]
NPT471	Organism	Trypanosoma brucei brucei	Trypanosoma brucei brucei	Inhibition	=	64.3	%	PMID[19581457]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC469758 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	22894
0.1-0.2	21358
0.2-0.3	4914
0.3-0.4	500
0.4-0.5	154
0.5-0.6	27
0.6-0.7	4
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.78	Intermediate Similarity	NPC469764
0.6863	Remote Similarity	NPC6407
0.6863	Remote Similarity	NPC545184
0.6604	Remote Similarity	NPC274784
0.6604	Remote Similarity	NPC20709
0.5818	Remote Similarity	NPC20354
0.5818	Remote Similarity	NPC150648
0.5818	Remote Similarity	NPC162869
0.5789	Remote Similarity	NPC18727
0.5741	Remote Similarity	NPC188243
0.5741	Remote Similarity	NPC110228
0.5714	Remote Similarity	NPC329203
0.5714	Remote Similarity	NPC222342
0.5484	Remote Similarity	NPC148757
0.5439	Remote Similarity	NPC73028
0.5439	Remote Similarity	NPC296917
0.5439	Remote Similarity	NPC156057
0.5439	Remote Similarity	NPC170907
0.5424	Remote Similarity	NPC302950
0.5397	Remote Similarity	NPC477840
0.5283	Remote Similarity	NPC99854
0.5254	Remote Similarity	NPC601395
0.5231	Remote Similarity	NPC108456
0.5217	Remote Similarity	NPC64915
0.5172	Remote Similarity	NPC480993
0.5172	Remote Similarity	NPC338131
0.5143	Remote Similarity	NPC219163
0.5088	Remote Similarity	NPC32441
0.5088	Remote Similarity	NPC243083
0.5088	Remote Similarity	NPC13768
0.5088	Remote Similarity	NPC287246
0.5088	Remote Similarity	NPC79943

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC469758 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3475
0.1-0.2	5376
0.2-0.3	287
0.3-0.4	7
0.4-0.5	2
0.5-0.6	3
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.5424	Remote Similarity	NPD1934	Phase 0
0.5088	Remote Similarity	NPD1550	Phase 2
0.5088	Remote Similarity	NPD1552	Clinical (unspecified phase)

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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