NPASS Compound

Natural Product: NPC54472

Natural Product ID	NPC54472
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	WACBUPFEGWUGPB-VOFPXKNKSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	129369931
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 9.5454 1.1485 1.3091 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7812 -0.0289 1.3614 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4113 -0.0370 1.1035 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7180 1.1112 0.7807 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3617 1.0870 0.5281 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6362 -0.0850 0.5863 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3345 -1.2300 0.9095 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6907 -1.2116 1.1631 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3856 -2.3917 1.4916 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1969 -0.1129 0.3185 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6531 -1.0844 -0.4837 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3651 -1.0981 -0.7152 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5368 -0.2030 -0.2045 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8331 -0.2415 -0.4681 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7229 0.6666 0.0415 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2208 1.6866 0.8719 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1150 1.7201 1.1260 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0117 0.7994 0.6084 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3611 0.8312 0.8636 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8386 1.7261 1.5985 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0621 0.6164 -0.2255 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6745 -0.3316 -1.0228 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.4332 0.2889 -2.1890 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.5982 -0.6121 -2.5080 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.5754 -0.4515 -1.3347 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.7797 -0.4225 -0.0327 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.5563 -1.2422 0.9762 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8674 -1.2979 2.1967 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5491 -1.0549 -0.1972 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2710 0.7440 -1.4349 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1481 -1.9371 -2.5021 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8243 1.5637 -1.7972 O 0 0 0 0 0 0 0 0 0 0 0 0 9.2327 1.8233 0.4822 H 0 0 0 0 0 0 0 0 0 0 0 0 10.6197 0.9599 1.1718 H 0 0 0 0 0 0 0 0 0 0 0 0 9.4404 1.7441 2.2512 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2225 2.0659 0.7170 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7992 1.9964 0.2698 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7845 -2.1688 0.9619 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8247 -3.0990 1.9542 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2963 -1.8427 -0.9264 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1322 -1.0748 -1.1277 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9124 2.3947 1.2695 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5557 2.4853 1.7601 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0034 -1.0866 -1.4594 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7329 0.3391 -3.0478 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1025 -0.3366 -3.4514 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3083 -1.2926 -1.3396 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7033 0.6056 0.3309 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5576 -0.7982 1.1511 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7114 -2.2861 0.6113 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0768 -0.7246 2.1199 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4797 0.9896 -2.3768 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8298 -2.5588 -2.1455 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0522 2.1685 -1.8954 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 6 10 1 0 10 11 2 0 11 12 1 0 12 13 1 0 13 14 2 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 15 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 19 10 1 0 29 22 1 0 18 13 1 0 1 33 1 0 1 34 1 0 1 35 1 0 4 36 1 0 5 37 1 0 7 38 1 0 9 39 1 0 11 40 1 0 14 41 1 0 16 42 1 0 17 43 1 0 22 44 1 6 23 45 1 6 24 46 1 6 25 47 1 1 26 48 1 1 27 49 1 0 27 50 1 0 28 51 1 0 30 52 1 0 31 53 1 0 32 54 1 0 M END

Standard InCHIKey	WACBUPFEGWUGPB-VOFPXKNKSA-N
Standard InCHI	InChI=1S/C22H22O10/c1-29-15-5-2-10(6-14(15)24)13-9-30-16-7-11(3-4-12(16)18(13)25)31-22-21(28)20(27)19(26)17(8-23)32-22/h2-7,9,17,19-24,26-28H,8H2,1H3/t17-,19-,20+,21-,22+/m1/s1
SMILES	COc1ccc(cc1O)c1coc2cc(ccc2c1=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
NPO24846	Astragalus membranaceus	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	DOI[10.1021/np50075a009]
NPO15715	Astragalus mongholicus	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	PMID[15763368]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	roots	purchased from Kiu Shun Trading Ltd., Vancouver, Canada	2000	PMID[16643021]
NPO24846	Astragalus membranaceus	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	PMID[17253088]
NPO24846	Astragalus membranaceus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25068786]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25538068]
NPO15715	Astragalus mongholicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25844502]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27400088]
NPO24846	Astragalus membranaceus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30758201]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36838931]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37480748]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24846	Astragalus membranaceus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15715	Astragalus mongholicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15715	Astragalus mongholicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24846	Astragalus membranaceus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15715	Astragalus mongholicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24846	Astragalus membranaceus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15715	Astragalus mongholicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15715	Astragalus mongholicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24846	Astragalus membranaceus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15715	Astragalus mongholicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO24846	Astragalus membranaceus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15462	Angelica sinensis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15715	Astragalus mongholicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20554	Astragalus complanatus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24846	Astragalus membranaceus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15462	Angelica sinensis	Species	Apiaceae	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 NPC54472 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	20434
0.1-0.2	25212
0.2-0.3	3046
0.3-0.4	884
0.4-0.5	222
0.5-0.6	37
0.6-0.7	13
0.7-0.8	1
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC229729
0.8333	Intermediate Similarity	NPC45165
0.7867	Intermediate Similarity	NPC161749
0.7595	Intermediate Similarity	NPC307518
0.7326	Intermediate Similarity	NPC51326
0.7273	Intermediate Similarity	NPC235575
0.725	Intermediate Similarity	NPC601607
0.6923	Remote Similarity	NPC135345
0.6753	Remote Similarity	NPC25547
0.675	Remote Similarity	NPC258035
0.6667	Remote Similarity	NPC73511
0.6625	Remote Similarity	NPC211014
0.6543	Remote Similarity	NPC105511
0.6341	Remote Similarity	NPC603782
0.631	Remote Similarity	NPC224462
0.6279	Remote Similarity	NPC479407
0.619	Remote Similarity	NPC100720
0.6092	Remote Similarity	NPC48773
0.6064	Remote Similarity	NPC231194
0.6	Remote Similarity	NPC205076
0.5977	Remote Similarity	NPC607201
0.5952	Remote Similarity	NPC197896
0.5952	Remote Similarity	NPC313163
0.5952	Remote Similarity	NPC156457
0.593	Remote Similarity	NPC479402
0.5862	Remote Similarity	NPC22832
0.5795	Remote Similarity	NPC150442
0.5765	Remote Similarity	NPC168822
0.5765	Remote Similarity	NPC234739
0.5618	Remote Similarity	NPC479406
0.5595	Remote Similarity	NPC487214
0.5568	Remote Similarity	NPC479401
0.5506	Remote Similarity	NPC43761
0.5506	Remote Similarity	NPC21666
0.5506	Remote Similarity	NPC486578
0.5506	Remote Similarity	NPC605067
0.5465	Remote Similarity	NPC259070
0.5455	Remote Similarity	NPC80710
0.5395	Remote Similarity	NPC181209
0.5393	Remote Similarity	NPC481043
0.5393	Remote Similarity	NPC80140
0.5349	Remote Similarity	NPC160515
0.5287	Remote Similarity	NPC58053
0.5283	Remote Similarity	NPC76047
0.5281	Remote Similarity	NPC138540
0.5263	Remote Similarity	NPC181124
0.5256	Remote Similarity	NPC25292
0.5227	Remote Similarity	NPC95090
0.5227	Remote Similarity	NPC27408
0.5222	Remote Similarity	NPC285197
0.5205	Remote Similarity	NPC182428
0.519	Remote Similarity	NPC103409
0.5169	Remote Similarity	NPC186807
0.5165	Remote Similarity	NPC120099
0.5128	Remote Similarity	NPC139293
0.5104	Remote Similarity	NPC479405
0.5052	Remote Similarity	NPC479404

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC54472 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4781
0.1-0.2	4266
0.2-0.3	88
0.3-0.4	9
0.4-0.5	4
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
0.7867	Intermediate Similarity	NPD4381	Clinical (unspecified phase)
0.5349	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