NPASS Compound

Natural Product: NPC552787

Natural Product ID	NPC552787
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	5-hydroxy-3-(4-hydroxyphenyl)-6-methoxy-7-[(2~{S},3~{R},4~{S},5~{S},6~{R})-3,4,5-trihydroxy-6-[[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxymethyl]tetrahydropyran-2-yl]oxy-chromen-4-one
IUPAC Name	5-hydroxy-3-(4-hydroxyphenyl)-6-methoxy-7-[(2~{S},3~{R},4~{S},5~{S},6~{R})-3,4,5-trihydroxy-6-[[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxymethyl]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]

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 76 80 0 0 0 0 0 0 0 0999 V2000 1.5549 2.5812 -1.1306 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0533 1.4918 -1.9215 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7604 0.5167 -1.2096 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1163 -0.6006 -0.7497 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8066 -0.9199 -0.9012 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2407 -0.3476 -1.5618 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1242 0.2134 -0.6763 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3345 0.5776 -1.1022 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3310 0.4304 0.0491 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6104 0.8015 -0.3576 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4783 0.6499 0.7223 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.4135 -0.3042 0.3483 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.3113 -0.6051 1.3598 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.4042 -1.4632 0.7534 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8499 -2.6300 0.2327 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8525 0.5950 2.0599 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.4642 0.6437 3.3942 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5490 1.8880 1.3376 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.3378 2.0536 0.2108 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0780 1.9825 1.0214 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.8525 2.8818 -0.0421 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9074 -0.0919 -2.2967 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.8102 0.7371 -2.9857 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9101 -0.6015 -3.2807 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5522 -1.4136 -4.2090 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8868 -1.3860 -2.4648 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0814 -1.9513 -3.2585 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9456 -1.5011 -0.0400 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2787 -1.2776 0.1692 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9934 -2.1770 0.8495 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2746 -2.0128 1.0787 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9691 -0.9088 0.6371 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3829 -0.8089 0.9349 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9647 0.3523 1.3943 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3104 0.4498 1.6786 C 0 0 0 0 0 0 0 0 0 0 0 0 11.1292 -0.6679 1.4978 C 0 0 0 0 0 0 0 0 0 0 0 0 12.4896 -0.6049 1.7746 O 0 0 0 0 0 0 0 0 0 0 0 0 10.5612 -1.8366 1.0388 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1987 -1.9050 0.7600 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2393 0.0251 -0.0661 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8179 1.0399 -0.4870 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8906 -0.1420 -0.3105 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1270 0.7602 -1.0039 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7364 1.9067 -1.4903 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3835 2.2534 -0.0854 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6785 3.0497 -1.5820 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3456 3.3815 -1.0745 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0884 0.4555 -2.2396 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3257 1.6876 -1.3212 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3802 -0.6312 0.3614 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0434 1.0249 0.9267 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9300 0.2793 1.6107 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7789 -1.2339 2.1032 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.2492 -1.6307 1.4229 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.8110 -0.9033 -0.1392 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9243 -2.7151 0.5661 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.9784 0.5019 2.0643 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0994 1.2851 3.8397 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8199 2.7120 2.0433 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8033 2.2329 -0.6031 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5436 2.4224 1.8882 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7073 2.3241 -0.8423 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5182 -0.9753 -1.9589 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1337 0.1821 -3.7555 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3589 0.2361 -3.7644 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8444 -1.9871 -4.6404 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4539 -2.1170 -1.8651 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3635 -2.8301 -2.8534 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4360 -2.3997 0.3333 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8085 -2.7826 1.6416 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3368 1.2202 1.5361 H 0 0 0 0 0 0 0 0 0 0 0 0 10.7860 1.3530 2.0403 H 0 0 0 0 0 0 0 0 0 0 0 0 13.1268 0.0200 1.2866 H 0 0 0 0 0 0 0 0 0 0 0 0 11.1948 -2.7011 0.8988 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7725 -2.8297 0.4013 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9996 2.6942 -0.9222 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 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 13 16 1 0 16 17 1 0 16 18 1 0 18 19 1 0 18 20 1 0 20 21 1 0 8 22 1 0 22 23 1 0 22 24 1 0 24 25 1 0 24 26 1 0 26 27 1 0 4 28 1 0 28 29 2 0 29 30 1 0 30 31 1 0 31 32 2 0 32 33 1 0 33 34 2 0 34 35 1 0 35 36 2 0 36 37 1 0 36 38 1 0 38 39 2 0 32 40 1 0 40 41 2 0 40 42 1 0 42 43 2 0 43 44 1 0 43 3 1 0 26 6 1 0 42 29 1 0 20 11 1 0 39 33 1 0 1 45 1 0 1 46 1 0 1 47 1 0 6 48 1 6 8 49 1 6 9 50 1 0 9 51 1 0 11 52 1 1 13 53 1 1 14 54 1 0 14 55 1 0 15 56 1 0 16 57 1 1 17 58 1 0 18 59 1 1 19 60 1 0 20 61 1 1 21 62 1 0 22 63 1 1 23 64 1 0 24 65 1 6 25 66 1 0 26 67 1 1 27 68 1 0 28 69 1 0 31 70 1 0 34 71 1 0 35 72 1 0 37 73 1 0 38 74 1 0 39 75 1 0 44 76 1 0 M END

Standard InCHIKey	DEAGIDFEDRILTP-CVGGESKWSA-N
Standard InCHI	InChI=1S/C28H32O16/c1-39-26-14(6-13-17(21(26)34)18(31)12(8-40-13)10-2-4-11(30)5-3-10)42-28-25(38)23(36)20(33)16(44-28)9-41-27-24(37)22(35)19(32)15(7-29)43-27/h2-6,8,15-16,19-20,22-25,27-30,32-38H,7,9H2,1H3/t15-,16-,19-,20-,22+,23+,24+,25-,27-,28-/m1/s1
SMILES	COC1=C(O[C@@H]2O[C@H](CO[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)[C@@H](O)[C@H](O)[C@H]2O)C=C2OC=C(C3=CC=C(O)C=C3)C(=O)C2=C1O

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
NPO15902	Iris spuria	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9325	Dalbergia volubilis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9429	Dalbergia sissoides	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9325	Dalbergia volubilis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15902	Iris spuria	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9325	Dalbergia volubilis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15902	Iris spuria	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9429	Dalbergia sissoides	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9325	Dalbergia volubilis	Species	Fabaceae	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 NPC552787 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	19474
0.1-0.2	25299
0.2-0.3	3826
0.3-0.4	970
0.4-0.5	233
0.5-0.6	39
0.6-0.7	11
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
0.8354	Intermediate Similarity	NPC205076
0.7907	Intermediate Similarity	NPC479405
0.7816	Intermediate Similarity	NPC479404
0.7126	Intermediate Similarity	NPC48773
0.6923	Remote Similarity	NPC303913
0.6818	Remote Similarity	NPC307518
0.6809	Remote Similarity	NPC257714
0.6782	Remote Similarity	NPC224462
0.6702	Remote Similarity	NPC479403
0.6628	Remote Similarity	NPC105511
0.6437	Remote Similarity	NPC197896
0.6437	Remote Similarity	NPC313163
0.618	Remote Similarity	NPC73511
0.6111	Remote Similarity	NPC100720
0.6067	Remote Similarity	NPC161749
0.5876	Remote Similarity	NPC475155
0.5842	Remote Similarity	NPC231194
0.5823	Remote Similarity	NPC216769
0.5778	Remote Similarity	NPC259070
0.5745	Remote Similarity	NPC99957
0.5699	Remote Similarity	NPC481043
0.5657	Remote Similarity	NPC204693
0.5652	Remote Similarity	NPC105025
0.5644	Remote Similarity	NPC51326
0.5604	Remote Similarity	NPC348541
0.5543	Remote Similarity	NPC156457
0.5495	Remote Similarity	NPC135345
0.5405	Remote Similarity	NPC473895
0.5376	Remote Similarity	NPC258035
0.5368	Remote Similarity	NPC80140
0.534	Remote Similarity	NPC483707
0.5333	Remote Similarity	NPC235575
0.5326	Remote Similarity	NPC45165
0.5319	Remote Similarity	NPC24043
0.5301	Remote Similarity	NPC57751
0.5294	Remote Similarity	NPC488073
0.5287	Remote Similarity	NPC60756
0.5269	Remote Similarity	NPC211014
0.5263	Remote Similarity	NPC117260
0.5213	Remote Similarity	NPC93337
0.5204	Remote Similarity	NPC479407
0.5158	Remote Similarity	NPC186807
0.5155	Remote Similarity	NPC229729
0.5152	Remote Similarity	NPC172807
0.5152	Remote Similarity	NPC211594
0.5104	Remote Similarity	NPC201292
0.5102	Remote Similarity	NPC479406
0.5098	Remote Similarity	NPC102028
0.5098	Remote Similarity	NPC156869
0.5093	Remote Similarity	NPC475261
0.5053	Remote Similarity	NPC234739
0.5052	Remote Similarity	NPC488071
0.5049	Remote Similarity	NPC473571
0.5049	Remote Similarity	NPC110941

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC552787 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5209
0.1-0.2	3867
0.2-0.3	61
0.3-0.4	5
0.4-0.5	7
0.5-0.6	0
0.6-0.7	1
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
0.6067	Remote Similarity	NPD4381	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