NPASS Compound

Natural Product: NPC208769

Natural Product ID	NPC208769
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	4-Hydroxy-3,5-Dimethoxyphenyl Beta-D-Glucopyranosyl-(1->6)-Beta-D-Glucopyranosyl-(1->6)-Beta-D-Glucopyranoside
IUPAC Name	(2R,3S,4S,5R,6R)-2-(hydroxymethyl)-6-[[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-[[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-(4-hydroxy-3,5-dimethoxyphenoxy)oxan-2-yl]methoxy]oxan-2-yl]methoxy]oxane-3,4,5-triol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL541965
PubChem CID	42638456
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0000198] Oligosaccharides

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 85 88 0 0 0 0 0 0 0 0999 V2000 -4.8679 3.8049 -0.1149 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4500 2.6346 -0.5370 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9437 2.2136 -1.9348 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5974 2.0264 -1.8946 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1318 0.8026 -2.3118 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.2082 -0.2108 -1.4279 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0419 -0.7330 -0.9432 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2306 -1.8610 0.0356 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9612 -2.2608 0.4338 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9484 -2.7289 1.7542 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7192 -1.6909 2.5877 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4270 -1.6451 3.3083 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7044 -1.6358 2.5047 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7177 -0.5421 1.6694 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9432 0.1302 1.6257 C 0 0 1 0 0 0 0 0 0 0 0 0 2.9547 1.0313 0.5965 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9041 1.0722 -0.3997 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8104 2.0316 -1.4208 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7166 2.1317 -2.4414 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6114 3.0888 -3.4499 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5322 4.0287 -3.4648 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7895 1.2623 -2.5019 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9281 0.3056 -1.5293 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9871 0.2281 -0.5003 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9914 -0.5871 -1.5538 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1077 -1.5721 -0.5261 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7460 1.3017 -3.5012 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0455 0.8339 2.9802 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2162 -0.2823 3.9968 C 0 0 2 0 0 0 0 0 0 0 0 0 2.8508 -1.6315 3.4957 C 0 0 2 0 0 0 0 0 0 0 0 0 3.9522 -2.3808 3.0309 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5904 0.0579 5.1948 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1455 1.7077 2.9872 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1802 -3.5426 2.0529 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4335 -2.7124 1.9817 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.1199 -1.4685 1.1851 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2993 -0.8914 0.7078 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9015 -2.3800 3.2631 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2704 -4.5913 1.1175 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6312 0.4820 -3.7068 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1675 0.4307 -3.6851 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.6613 0.9645 -2.3533 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.0470 1.1361 -2.3776 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.6197 -0.8383 -3.9450 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2834 1.4729 -4.6176 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5432 3.7788 0.8269 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2165 1.8391 0.2017 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5517 2.7511 -0.5565 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2153 3.0869 -2.5797 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0156 0.9814 -2.4579 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3112 -1.0527 -1.6970 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5417 0.0885 -0.3650 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6975 -2.7584 -0.4429 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0804 -3.4314 1.8031 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4224 -0.6964 3.8963 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4329 -2.4619 4.0776 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8390 -2.5436 1.8820 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7439 -0.5938 1.5545 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9680 2.7147 -1.3729 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7082 4.7528 -2.6409 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5725 4.5829 -4.4283 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5603 3.5033 -3.3132 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1518 -0.5490 0.2395 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1933 -1.0639 0.4510 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2442 -2.2646 -0.5475 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0123 -2.1790 -0.7017 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7343 1.1583 -3.3207 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1526 1.4216 3.1956 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3201 -0.3046 4.2359 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4923 -2.2275 4.3876 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6302 -3.0054 2.3162 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2078 0.4232 5.8659 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4554 1.7368 3.9384 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1573 -4.0219 3.0352 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2001 -3.3041 1.4387 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6348 -0.6762 1.7921 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1058 -1.3097 1.0624 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1128 -2.3399 3.8556 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4916 -4.6142 0.5271 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2919 -0.4683 -4.1008 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5391 1.1124 -4.4674 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4725 0.1839 -1.5927 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2502 1.6660 -3.2027 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5487 -0.9234 -3.6706 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8208 2.2958 -4.4957 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 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 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 1 0 20 21 1 0 19 22 2 0 22 23 1 0 23 24 2 0 23 25 1 0 25 26 1 0 22 27 1 0 15 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 29 32 1 0 28 33 1 0 10 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 35 38 1 0 34 39 1 0 5 40 1 0 40 41 1 0 41 42 1 0 42 43 1 0 41 44 1 0 40 45 1 0 42 3 1 0 36 8 1 0 30 13 1 0 24 17 1 0 1 46 1 0 2 47 1 0 2 48 1 0 3 49 1 6 5 50 1 6 7 51 1 0 7 52 1 0 8 53 1 6 10 54 1 6 12 55 1 0 12 56 1 0 13 57 1 6 15 58 1 6 18 59 1 0 21 60 1 0 21 61 1 0 21 62 1 0 24 63 1 0 26 64 1 0 26 65 1 0 26 66 1 0 27 67 1 0 28 68 1 1 29 69 1 1 30 70 1 1 31 71 1 0 32 72 1 0 33 73 1 0 34 74 1 1 35 75 1 6 36 76 1 1 37 77 1 0 38 78 1 0 39 79 1 0 40 80 1 6 41 81 1 6 42 82 1 1 43 83 1 0 44 84 1 0 45 85 1 0 M END

Standard InCHIKey	XSZKQQFUCZZITK-XVWRWHHWSA-N
Standard InCHI	InChI=1S/C26H40O19/c1-38-9-3-8(4-10(39-2)14(9)28)42-26-23(37)20(34)17(31)13(45-26)7-41-25-22(36)19(33)16(30)12(44-25)6-40-24-21(35)18(32)15(29)11(5-27)43-24/h3-4,11-13,15-37H,5-7H2,1-2H3/t11-,12-,13-,15-,16-,17-,18+,19+,20+,21-,22-,23-,24-,25-,26-/m1/s1
SMILES	OC[C@H]1O[C@@H](OC[C@H]2O[C@@H](OC[C@H]3O[C@@H](Oc4cc(OC)c(c(c4)OC)O)[C@@H]([C@H]([C@@H]3O)O)O)[C@@H]([C@H]([C@@H]2O)O)O)[C@@H]([C@H]([C@@H]1O)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
NPO33268	wheat	n.a.	n.a.	n.a.	wheat germ	n.a.	n.a.	PMID[19284743]
NPO33268	wheat	n.a.	n.a.	n.a.	wheat bran	n.a.	n.a.	PMID[21658963]
NPO33268	wheat	n.a.	n.a.	n.a.	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
Activity	1

Activity Type	# Activity
Non-molecular	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
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	Activity	=	0.8	n.a.	PMID[19284743]

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 NPC208769 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	22261
0.1-0.2	23184
0.2-0.3	2949
0.3-0.4	1114
0.4-0.5	311
0.5-0.6	25
0.6-0.7	3
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9804	High Similarity	NPC189589
0.7966	Intermediate Similarity	NPC287780
0.7966	Intermediate Similarity	NPC60982
0.7797	Intermediate Similarity	NPC37074
0.7308	Intermediate Similarity	NPC192810
0.7241	Intermediate Similarity	NPC57751
0.6825	Remote Similarity	NPC60756
0.6061	Remote Similarity	NPC87696
0.6	Remote Similarity	NPC469622
0.5692	Remote Similarity	NPC171533
0.5667	Remote Similarity	NPC221090
0.5641	Remote Similarity	NPC46958
0.5455	Remote Similarity	NPC145112
0.5439	Remote Similarity	NPC276195
0.5422	Remote Similarity	NPC213052
0.5395	Remote Similarity	NPC602634
0.5345	Remote Similarity	NPC217854
0.5333	Remote Similarity	NPC168358
0.5301	Remote Similarity	NPC164047
0.5301	Remote Similarity	NPC470452
0.5301	Remote Similarity	NPC102028
0.5301	Remote Similarity	NPC470453
0.5301	Remote Similarity	NPC63105
0.5294	Remote Similarity	NPC298845
0.5286	Remote Similarity	NPC469621
0.527	Remote Similarity	NPC3293
0.525	Remote Similarity	NPC61791
0.5231	Remote Similarity	NPC132895
0.5211	Remote Similarity	NPC213723
0.5161	Remote Similarity	NPC470270
0.5161	Remote Similarity	NPC145900
0.5139	Remote Similarity	NPC119125
0.5135	Remote Similarity	NPC197708
0.5085	Remote Similarity	NPC484157

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC208769 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6228
0.1-0.2	2827
0.2-0.3	66
0.3-0.4	24
0.4-0.5	5
0.5-0.6	0
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
		NPD

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