NPASS Compound

Natural Product: NPC25817

Natural Product ID	NPC25817
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	1,4-Di-O-Beta-D-Glucopyranosyloxy-2-Methoxybenzene
IUPAC Name	(2R,3S,4S,5R,6S)-2-(hydroxymethyl)-6-[3-methoxy-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenoxy]oxane-3,4,5-triol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL226820
PubChem CID	16681195
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0004165] Phenolic 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 60 62 0 0 0 0 0 0 0 0999 V2000 -1.3977 2.1050 -2.3833 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7194 1.1892 -1.3643 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7726 0.4760 -0.6441 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5752 0.6312 -0.8958 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5708 -0.0624 -0.1999 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1225 -0.9237 0.7672 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2213 -1.0965 1.0379 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2066 -0.3894 0.3266 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4963 -0.5823 0.6160 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7087 -0.1354 0.2022 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.5096 -1.3573 -0.2473 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9567 -1.0540 -0.4351 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.5040 -0.2138 0.7213 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.5756 0.9753 0.8483 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.1582 1.9852 1.8098 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3735 2.4087 1.2570 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3488 0.4770 1.2986 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8046 0.1336 0.4514 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6761 -2.2478 -0.4178 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9479 -1.7770 -1.4489 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8907 0.1377 -0.4989 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0267 -0.4402 0.0614 C 0 0 1 0 0 0 0 0 0 0 0 0 4.8171 -1.2469 -0.9550 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9848 -0.4788 -1.4940 C 0 0 2 0 0 0 0 0 0 0 0 0 6.9019 -0.1900 -0.3235 C 0 0 1 0 0 0 0 0 0 0 0 0 6.1160 0.0146 0.9537 C 0 0 1 0 0 0 0 0 0 0 0 0 6.8703 0.8702 1.9383 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2076 0.9064 3.1436 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8373 0.4883 0.7127 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7347 -1.2916 -0.1447 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5696 0.6927 -2.1227 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3153 -2.3759 -0.3132 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3519 2.4304 -2.8461 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9767 3.0284 -1.8972 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6862 1.7244 -3.1133 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9112 1.3144 -1.6618 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8746 -1.4909 1.3400 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5747 -1.7725 1.7971 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7447 0.6066 -0.6054 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4041 -2.1255 0.5436 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1772 -0.5100 -1.3711 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4122 -0.8485 1.6451 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4440 1.4609 -0.1270 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5235 2.8677 1.9131 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4061 1.4959 2.7798 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2934 2.5707 0.2825 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3985 -0.3881 1.0627 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4092 -2.8542 -1.1502 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0679 -1.0262 -2.0965 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7190 -1.1486 0.8508 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1075 -1.5460 -1.7400 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5195 -1.1044 -2.2136 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5062 0.7177 -0.4927 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0055 -0.9847 1.4238 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8505 0.3445 2.1204 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1343 1.8659 1.5413 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5030 1.6257 3.1370 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2607 -1.5146 -0.9380 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5841 0.7915 -1.9706 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7309 -3.1583 -0.4714 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 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 14 17 1 0 13 18 1 0 12 19 1 0 11 20 1 0 5 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 26 29 1 0 25 30 1 0 24 31 1 0 23 32 1 0 8 3 1 0 17 10 1 0 29 22 1 0 1 33 1 0 1 34 1 0 1 35 1 0 4 36 1 0 6 37 1 0 7 38 1 0 10 39 1 6 11 40 1 1 12 41 1 6 13 42 1 1 14 43 1 6 15 44 1 0 15 45 1 0 16 46 1 0 18 47 1 0 19 48 1 0 20 49 1 0 22 50 1 1 23 51 1 6 24 52 1 6 25 53 1 6 26 54 1 1 27 55 1 0 27 56 1 0 28 57 1 0 30 58 1 0 31 59 1 0 32 60 1 0 M END

Standard InCHIKey	XYTIVPVWLLNVKO-SKYGPZSASA-N
Standard InCHI	InChI=1S/C19H28O13/c1-28-9-4-7(29-18-16(26)14(24)12(22)10(5-20)31-18)2-3-8(9)30-19-17(27)15(25)13(23)11(6-21)32-19/h2-4,10-27H,5-6H2,1H3/t10-,11-,12-,13-,14+,15+,16-,17-,18-,19-/m1/s1
SMILES	COc1cc(ccc1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)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
NPO30984	Fraxinus sieboldiana	Species	Oleaceae	Eukaryota	stem bark	n.a.	n.a.	PMID[17461599]
NPO30984	Fraxinus sieboldiana	Species	Oleaceae	Eukaryota	n.a.	stem	n.a.	PMID[20961093]
NPO30984	Fraxinus sieboldiana	Species	Oleaceae	Eukaryota	Stem bark	Lu Mountain, Jiangxi Province, China	2004-AUG	PMID[20961093]
NPO30984	Fraxinus sieboldiana	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26697686]
NPO30984	Fraxinus sieboldiana	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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
Inhibition	1
IC50	4

Activity Type	# Activity
Cell line	3
Subcellular	1
Others	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
NPT179	Cell line	A2780	Homo sapiens	IC50	>	5000.0	nM	PMID[17722904]
NPT180	Cell line	HCT-8	Homo sapiens	IC50	>	5000.0	nM	PMID[23301897]
NPT81	Cell line	A549	Homo sapiens	IC50	>	5000.0	nM	DOI[10.6019/CHEMBL1201861]
NPT1084	Subcellular	Liver microsomes	Rattus norvegicus	IC50	>	10000.0	nM	PMID[17844994]
NPT2	Others	Unspecified	n.a.	Inhibition	=	16.3	%	DrugMatrix in vivo data: Hematology

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 NPC25817 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	15831
0.1-0.2	30207
0.2-0.3	2791
0.3-0.4	620
0.4-0.5	320
0.5-0.6	55
0.6-0.7	13
0.7-0.8	0
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
0.9268	High Similarity	NPC153149
0.7843	Intermediate Similarity	NPC247146
0.75	Intermediate Similarity	NPC276195
0.7381	Intermediate Similarity	NPC228907
0.7333	Intermediate Similarity	NPC217854
0.6939	Remote Similarity	NPC145900
0.66	Remote Similarity	NPC221090
0.6471	Remote Similarity	NPC166040
0.6458	Remote Similarity	NPC192810
0.6383	Remote Similarity	NPC142319
0.6111	Remote Similarity	NPC472024
0.6111	Remote Similarity	NPC270849
0.6071	Remote Similarity	NPC104167
0.6042	Remote Similarity	NPC212729
0.6042	Remote Similarity	NPC604498
0.6	Remote Similarity	NPC26653
0.6	Remote Similarity	NPC80600
0.6	Remote Similarity	NPC152722
0.5926	Remote Similarity	NPC218685
0.5918	Remote Similarity	NPC269242
0.5893	Remote Similarity	NPC248355
0.5882	Remote Similarity	NPC299144
0.5882	Remote Similarity	NPC609376
0.5818	Remote Similarity	NPC479028
0.5818	Remote Similarity	NPC23084
0.5818	Remote Similarity	NPC479031
0.58	Remote Similarity	NPC294470
0.5789	Remote Similarity	NPC55040
0.5741	Remote Similarity	NPC9912
0.569	Remote Similarity	NPC302378
0.5667	Remote Similarity	NPC37468
0.566	Remote Similarity	NPC69513
0.5614	Remote Similarity	NPC479029
0.5577	Remote Similarity	NPC60589
0.5577	Remote Similarity	NPC469708
0.5577	Remote Similarity	NPC604439
0.5556	Remote Similarity	NPC48863
0.5556	Remote Similarity	NPC95292
0.5556	Remote Similarity	NPC251981
0.5556	Remote Similarity	NPC13745
0.55	Remote Similarity	NPC276753
0.55	Remote Similarity	NPC205796
0.5472	Remote Similarity	NPC200092
0.5472	Remote Similarity	NPC226712
0.5469	Remote Similarity	NPC108674
0.5455	Remote Similarity	NPC215833
0.5439	Remote Similarity	NPC210478
0.541	Remote Similarity	NPC479030
0.541	Remote Similarity	NPC246947
0.541	Remote Similarity	NPC604095
0.5385	Remote Similarity	NPC9248
0.537	Remote Similarity	NPC80098
0.5357	Remote Similarity	NPC49074
0.5345	Remote Similarity	NPC473044
0.5294	Remote Similarity	NPC484157
0.5273	Remote Similarity	NPC214454
0.5263	Remote Similarity	NPC162093
0.5263	Remote Similarity	NPC604356
0.5185	Remote Similarity	NPC12308
0.5185	Remote Similarity	NPC608788
0.5179	Remote Similarity	NPC310661
0.5172	Remote Similarity	NPC214910
0.5167	Remote Similarity	NPC473045
0.5167	Remote Similarity	NPC232673
0.5167	Remote Similarity	NPC112766
0.5167	Remote Similarity	NPC604162
0.5161	Remote Similarity	NPC37074
0.5156	Remote Similarity	NPC99233
0.5079	Remote Similarity	NPC60756
0.5079	Remote Similarity	NPC287780
0.5079	Remote Similarity	NPC60982
0.5079	Remote Similarity	NPC604892
0.5077	Remote Similarity	NPC148273

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC25817 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5392
0.1-0.2	3620
0.2-0.3	109
0.3-0.4	26
0.4-0.5	2
0.5-0.6	1
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
0.5472	Remote Similarity	NPD1091	Pre-clinical

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