NPASS Compound

Natural Product: NPC566722

Natural Product ID	NPC566722
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3-(4-hydroxyphenyl)-7-methoxy-5-[(2~{S},3~{R},4~{S},5~{S},6~{S})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-chromen-4-one
IUPAC Name	3-(4-hydroxyphenyl)-7-methoxy-5-[(2~{S},3~{R},4~{S},5~{S},6~{S})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-chromen-4-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0000507] Isoflavonoid O-glycosides

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 54 57 0 0 0 0 0 0 0 0999 V2000 -1.3733 3.5033 -4.3372 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0345 3.4685 -3.9362 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4732 2.6868 -2.9234 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2905 1.8241 -2.1635 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2021 1.0398 -1.1518 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5158 0.1778 -0.3803 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8904 -0.1048 -0.4355 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4333 0.2844 0.7795 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7448 -0.1060 0.9413 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.6430 0.3566 -0.1759 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9336 -0.1024 0.1106 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7470 -1.6155 1.0777 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.9783 -2.0610 1.4854 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2969 -2.1887 -0.2252 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.0496 -3.5643 -0.0071 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0314 -1.5787 -0.6996 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9970 -1.7268 -2.1063 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5728 1.1215 -0.8729 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1057 0.3448 0.1413 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3641 -0.4385 0.8183 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4502 0.4496 0.3873 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0621 -0.3496 1.4483 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9574 0.2052 2.3393 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5460 -0.5344 3.3489 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2539 -1.8738 3.5027 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8380 -2.6353 4.5151 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3587 -2.4281 2.6115 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7710 -1.6914 1.6042 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1754 1.3217 -0.3936 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6428 2.0383 -1.3403 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3590 1.9820 -1.6242 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8189 2.7637 -2.6458 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6348 2.7376 -5.0831 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5692 4.4953 -4.8073 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0050 3.4589 -3.4316 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3415 1.7867 -2.4056 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3389 0.5061 -1.2406 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1223 0.3398 1.8822 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6733 1.4604 -0.1467 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3171 -0.0189 -1.1667 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4273 -0.3422 -0.7171 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9470 -1.8500 1.8380 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3905 -1.3584 2.0443 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1040 -2.1661 -0.9928 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7054 -3.8676 0.6863 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1464 -2.1386 -0.3303 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3980 -0.9070 -2.5343 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1950 1.2603 2.2274 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2559 -0.0982 4.0571 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7541 -3.0695 4.3561 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1073 -3.4771 2.7041 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0638 -2.1078 0.8918 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2497 1.3815 -0.1702 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5026 3.4058 -3.1804 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 9 12 1 0 12 13 1 0 12 14 1 0 14 15 1 0 14 16 1 0 16 17 1 0 5 18 2 0 18 19 1 0 19 20 2 0 19 21 1 0 21 22 1 0 22 23 2 0 23 24 1 0 24 25 2 0 25 26 1 0 25 27 1 0 27 28 2 0 21 29 2 0 29 30 1 0 30 31 1 0 31 32 2 0 32 3 1 0 16 7 1 0 31 18 1 0 28 22 1 0 1 33 1 0 1 34 1 0 1 35 1 0 4 36 1 0 7 37 1 6 9 38 1 1 10 39 1 0 10 40 1 0 11 41 1 0 12 42 1 1 13 43 1 0 14 44 1 6 15 45 1 0 16 46 1 1 17 47 1 0 23 48 1 0 24 49 1 0 26 50 1 0 27 51 1 0 28 52 1 0 29 53 1 0 32 54 1 0 M END

Standard InCHIKey	AJAGLPDYKVWJQE-GVJIXFOXSA-N
Standard InCHI	InChI=1S/C22H22O10/c1-29-12-6-14-17(18(25)13(9-30-14)10-2-4-11(24)5-3-10)15(7-12)31-22-21(28)20(27)19(26)16(8-23)32-22/h2-7,9,16,19-24,26-28H,8H2,1H3/t16-,19+,20-,21+,22+/m0/s1
SMILES	COC1=CC(O[C@@H]2O[C@@H](CO)[C@@H](O)[C@H](O)[C@H]2O)=C2C(=O)C(C3=CC=C(O)C=C3)=COC2=C1

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
NPO24693	Prunus cerasus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9917288]
NPO24693	Prunus cerasus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24693	Prunus cerasus	Species	Rosaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO24693	Prunus cerasus	Species	Rosaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO24693	Prunus cerasus	Species	Rosaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO24693	Prunus cerasus	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO24693	Prunus cerasus	Species	Rosaceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO24693	Prunus cerasus	Species	Rosaceae	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

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

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 NPC566722 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	22455
0.1-0.2	23225
0.2-0.3	2938
0.3-0.4	941
0.4-0.5	234
0.5-0.6	36
0.6-0.7	16
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.942	High Similarity	NPC100720
0.7922	Intermediate Similarity	NPC479407
0.7792	Intermediate Similarity	NPC479406
0.7368	Intermediate Similarity	NPC197896
0.7368	Intermediate Similarity	NPC105511
0.7368	Intermediate Similarity	NPC313163
0.7368	Intermediate Similarity	NPC161749
0.7308	Intermediate Similarity	NPC479402
0.7179	Intermediate Similarity	NPC205076
0.6765	Remote Similarity	NPC162680
0.6625	Remote Similarity	NPC73511
0.6463	Remote Similarity	NPC479401
0.6456	Remote Similarity	NPC45165
0.6296	Remote Similarity	NPC258035
0.625	Remote Similarity	NPC479405
0.625	Remote Similarity	NPC135345
0.622	Remote Similarity	NPC610763
0.619	Remote Similarity	NPC229729
0.618	Remote Similarity	NPC479404
0.6173	Remote Similarity	NPC259070
0.6173	Remote Similarity	NPC211014
0.6173	Remote Similarity	NPC348541
0.6098	Remote Similarity	NPC156457
0.6071	Remote Similarity	NPC80140
0.6047	Remote Similarity	NPC48773
0.5882	Remote Similarity	NPC169404
0.5882	Remote Similarity	NPC176186
0.5854	Remote Similarity	NPC183357
0.5747	Remote Similarity	NPC307518
0.5714	Remote Similarity	NPC234739
0.5698	Remote Similarity	NPC481043
0.5698	Remote Similarity	NPC224462
0.5581	Remote Similarity	NPC182045
0.5529	Remote Similarity	NPC603782
0.5455	Remote Similarity	NPC284960
0.5455	Remote Similarity	NPC601607
0.5412	Remote Similarity	NPC110349
0.5412	Remote Similarity	NPC83283
0.5402	Remote Similarity	NPC138540
0.5393	Remote Similarity	NPC150442
0.5393	Remote Similarity	NPC607201
0.5376	Remote Similarity	NPC303913
0.5294	Remote Similarity	NPC160515
0.5278	Remote Similarity	NPC223354
0.5278	Remote Similarity	NPC608360
0.527	Remote Similarity	NPC7013
0.5233	Remote Similarity	NPC39360
0.5233	Remote Similarity	NPC29763
0.5233	Remote Similarity	NPC210003
0.5208	Remote Similarity	NPC479403
0.519	Remote Similarity	NPC62518
0.5172	Remote Similarity	NPC93337
0.5172	Remote Similarity	NPC297987
0.5172	Remote Similarity	NPC323593
0.5172	Remote Similarity	NPC203500
0.5119	Remote Similarity	NPC25547
0.5114	Remote Similarity	NPC22195
0.5114	Remote Similarity	NPC24043
0.5114	Remote Similarity	NPC21190
0.5114	Remote Similarity	NPC105025
0.5056	Remote Similarity	NPC599850

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC566722 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5203
0.1-0.2	3842
0.2-0.3	89
0.3-0.4	12
0.4-0.5	2
0.5-0.6	1
0.6-0.7	0
0.7-0.8	1
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
0.7368	Intermediate Similarity	NPD4381	Clinical (unspecified phase)
0.5476	Remote Similarity	NPD3818	Discontinued

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