NPASS Compound

Natural Product: NPC61594

Natural Product ID	NPC61594
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Scorzodihydrostilbene D
IUPAC Name	1-[2-[2-(3,4-dimethoxyphenyl)ethyl]-6-hydroxy-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenyl]ethanone
Synonyms	Scorzodihydrostilbene D
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL563870
PubChem CID	42638805
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000253] Stilbenes [CHEMONTID:0000142] Stilbene 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 64 66 0 0 0 0 0 0 0 0999 V2000 5.1601 -2.9541 -2.1770 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5536 -2.0191 -1.2524 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5437 -1.7802 -0.1670 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3142 -1.3213 -0.6718 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7942 -0.5107 0.3723 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7038 0.2235 -0.0266 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5994 1.5932 -0.0979 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6052 2.4675 0.2294 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4750 3.8540 0.1486 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2852 4.3686 -0.2784 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2472 3.5344 -0.6179 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4051 2.1829 -0.5283 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7426 1.2844 -0.9036 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3321 0.7879 0.3952 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4803 -0.1145 0.1643 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2695 -1.4693 0.0374 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3485 -2.3071 -0.1785 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6292 -1.8076 -0.2683 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8500 -0.4504 -0.1422 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7698 0.3819 0.0731 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1461 0.0786 -0.2305 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3234 1.4733 -0.0952 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7185 -2.6231 -0.4827 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.6266 -4.0262 -0.6285 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9916 4.1666 -1.0650 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2191 4.4336 -2.2653 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0168 4.5035 -0.0539 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1816 5.7669 -0.3501 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5227 -1.3928 1.5796 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8908 -2.8395 1.3123 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2627 -2.9722 0.6837 C 0 0 2 0 0 0 0 0 0 0 0 0 5.2704 -3.0691 1.6416 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9282 -3.3501 0.4317 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1467 -0.9122 2.7281 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5319 -2.7791 -3.0931 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4969 -2.3141 -0.7629 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7638 -1.0099 -1.7104 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9837 -0.9929 0.5107 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6386 0.1393 0.6570 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5649 2.1004 0.5726 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2894 4.5173 0.4144 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3650 0.4085 -1.4572 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4897 1.8756 -1.4707 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5430 0.2003 0.9068 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6274 1.6388 1.0581 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2707 -1.8993 0.1030 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1473 -3.3685 -0.2737 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9106 1.4504 0.1760 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4114 1.6807 0.0762 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8058 1.8515 0.8153 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9303 1.9471 -1.0043 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6314 -4.3701 -0.9930 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8400 -4.2151 -1.4033 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3535 -4.5040 0.3192 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6751 4.3223 0.9785 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2967 5.5893 -0.0929 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9677 3.9532 -0.2142 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5905 6.1967 -1.1828 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4285 -1.3605 1.7480 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8924 -3.3741 2.2769 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2756 -3.8836 0.0465 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3557 -3.9600 2.0356 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1019 -3.5657 0.9394 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9262 -1.4558 2.9946 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 2 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 19 21 1 0 21 22 1 0 18 23 1 0 23 24 1 0 11 25 1 0 25 26 2 0 25 27 1 0 10 28 1 0 5 29 1 0 29 30 1 0 30 31 1 0 31 32 1 0 30 33 1 0 29 34 1 0 31 3 1 0 12 7 1 0 20 15 1 0 1 35 1 0 2 36 1 0 2 37 1 0 3 38 1 1 5 39 1 1 8 40 1 0 9 41 1 0 13 42 1 0 13 43 1 0 14 44 1 0 14 45 1 0 16 46 1 0 17 47 1 0 20 48 1 0 22 49 1 0 22 50 1 0 22 51 1 0 24 52 1 0 24 53 1 0 24 54 1 0 27 55 1 0 27 56 1 0 27 57 1 0 28 58 1 0 29 59 1 1 30 60 1 1 31 61 1 6 32 62 1 0 33 63 1 0 34 64 1 0 M END

Standard InCHIKey	PINFMINPJPEGSH-PFKOEMKTSA-N
Standard InCHI	InChI=1S/C24H30O10/c1-12(26)20-14(6-4-13-5-8-17(31-2)18(10-13)32-3)16(9-7-15(20)27)33-24-23(30)22(29)21(28)19(11-25)34-24/h5,7-10,19,21-25,27-30H,4,6,11H2,1-3H3/t19-,21-,22+,23-,24-/m1/s1
SMILES	OC[C@H]1O[C@@H](Oc2ccc(c(c2CCc2ccc(c(c2)OC)OC)C(=O)C)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
NPO10471	Scorzonera radiata	Species	Asteraceae	Eukaryota	n.a.	Mongolian	n.a.	PMID[19271716]
NPO10471	Scorzonera radiata	Species	Asteraceae	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

Activity Type	# Activity
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
NPT1	Others	Radical scavenging activity	n.a.	IC50	=	730990.0	nM	PMID[18494522]

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 NPC61594 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	15754
0.1-0.2	27202
0.2-0.3	5845
0.3-0.4	770
0.4-0.5	243
0.5-0.6	28
0.6-0.7	5
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8088	Intermediate Similarity	NPC56735
0.6622	Remote Similarity	NPC147596
0.6164	Remote Similarity	NPC177742
0.6119	Remote Similarity	NPC270849
0.6029	Remote Similarity	NPC26653
0.6027	Remote Similarity	NPC210192
0.5949	Remote Similarity	NPC476203
0.5882	Remote Similarity	NPC472024
0.5797	Remote Similarity	NPC80600
0.56	Remote Similarity	NPC475096
0.5588	Remote Similarity	NPC9912
0.5522	Remote Similarity	NPC69513
0.5429	Remote Similarity	NPC23084
0.5405	Remote Similarity	NPC611586
0.5375	Remote Similarity	NPC227902
0.5362	Remote Similarity	NPC215833
0.5316	Remote Similarity	NPC158635
0.5316	Remote Similarity	NPC229882
0.5286	Remote Similarity	NPC218685
0.527	Remote Similarity	NPC475628
0.5256	Remote Similarity	NPC148273
0.5217	Remote Similarity	NPC166040
0.5211	Remote Similarity	NPC205054
0.52	Remote Similarity	NPC134260
0.5195	Remote Similarity	NPC189115
0.5176	Remote Similarity	NPC299706
0.5176	Remote Similarity	NPC115466
0.5176	Remote Similarity	NPC61604
0.5135	Remote Similarity	NPC97326
0.5128	Remote Similarity	NPC99233
0.5075	Remote Similarity	NPC152722
0.5068	Remote Similarity	NPC479029
0.5063	Remote Similarity	NPC30432
0.5063	Remote Similarity	NPC605700

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC61594 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3954
0.1-0.2	4962
0.2-0.3	217
0.3-0.4	14
0.4-0.5	3
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