NPASS Compound

Natural Product: NPC190429

Natural Product ID	NPC190429
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	HSTZMXCBWJGKHG-UABZBGRASA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	11968839
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 50 52 0 0 0 0 0 0 0 0999 V2000 3.2032 -0.1802 0.2845 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7975 0.9202 0.8411 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4262 1.4073 0.9092 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1327 2.6087 1.5391 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1281 3.1152 1.6346 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1738 2.4138 1.0848 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9430 1.1928 0.4345 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3659 0.7185 0.3642 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0365 0.5475 -0.0911 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0832 -0.6630 -0.7770 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6123 -0.5001 -2.1982 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1207 -0.7003 -2.2418 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.7683 -0.2249 -0.9724 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0780 -0.8185 0.2365 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0845 -1.7105 0.9291 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5393 -2.3176 2.0696 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9743 -1.5732 -0.1559 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7246 1.1625 -0.9464 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4381 -2.0222 -2.5382 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3589 0.7970 -2.6410 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4154 4.3251 2.2703 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5854 -0.6575 0.2236 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6508 0.0264 0.7666 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9595 -0.4636 0.6875 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2327 -1.6577 0.0586 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1737 -2.3490 -0.4876 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8888 -1.8610 -0.4060 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5427 -2.1548 -0.0243 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4545 -0.8058 -0.1784 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5772 1.5446 1.3080 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9677 3.1624 1.9746 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1758 2.8124 1.1585 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5496 -0.2173 -0.1332 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0805 -1.0938 -0.8686 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1486 -1.2340 -2.8942 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5151 -0.0803 -3.0732 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8437 -0.5078 -1.0289 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7843 -0.0022 0.9291 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4380 -2.5059 0.2554 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9741 -1.1286 1.2375 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4357 -1.6822 2.8116 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1986 1.5471 -0.1706 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5611 -2.1762 -3.5036 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6095 1.4092 -1.9106 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0142 5.1522 1.8322 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4889 0.9641 1.2684 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7934 0.0729 1.1132 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3902 -3.2888 -0.9823 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0481 -2.4215 -0.8462 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0294 -2.2849 0.8472 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 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 7 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 1 22 1 0 22 23 2 0 23 24 1 0 24 25 2 0 25 26 1 0 26 27 2 0 25 28 1 0 8 3 1 0 17 10 1 0 27 22 1 0 1 29 1 0 2 30 1 0 4 31 1 0 6 32 1 0 8 33 1 0 10 34 1 6 11 35 1 6 12 36 1 6 13 37 1 6 14 38 1 1 15 39 1 0 15 40 1 0 16 41 1 0 18 42 1 0 19 43 1 0 20 44 1 0 21 45 1 0 23 46 1 0 24 47 1 0 26 48 1 0 27 49 1 0 28 50 1 0 M END

Standard InCHIKey	HSTZMXCBWJGKHG-UABZBGRASA-N
Standard InCHI	InChI=1S/C20H22O8/c21-10-16-17(24)18(25)19(26)20(28-16)27-15-8-12(7-14(23)9-15)2-1-11-3-5-13(22)6-4-11/h1-9,16-26H,10H2/b2-1+/t16-,17-,18+,19-,20+/m1/s1
SMILES	C(=Cc1cc(cc(c1)O[C@@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)/c1ccc(cc1)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
NPO9722	Strongylodesma aliwaliensis	n.a.	n.a.	n.a.	n.a.	South African	n.a.	PMID[15844938]
NPO2183	Eucalyptus sideroxylon	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36840164]
NPO2183	Eucalyptus sideroxylon	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22505	Bombax ceiba	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9722	Strongylodesma aliwaliensis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO4884	Caulerpa bikinensis	Species	Caulerpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22505	Bombax ceiba	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22505	Bombax ceiba	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9722	Strongylodesma aliwaliensis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO4081	Aspilia floribunda	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2183	Eucalyptus sideroxylon	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4884	Caulerpa bikinensis	Species	Caulerpaceae	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 NPC190429 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	21560
0.1-0.2	23245
0.2-0.3	3906
0.3-0.4	777
0.4-0.5	276
0.5-0.6	56
0.6-0.7	15
0.7-0.8	0
0.8-0.85	4
0.85-0.9	3
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC85799
1.0	High Similarity	NPC303422
0.8571	High Similarity	NPC242028
0.8571	High Similarity	NPC203230
0.8545	High Similarity	NPC218003
0.8246	Intermediate Similarity	NPC294166
0.8246	Intermediate Similarity	NPC115022
0.8136	Intermediate Similarity	NPC212770
0.8	Intermediate Similarity	NPC214910
0.7797	Intermediate Similarity	NPC8497
0.7541	Intermediate Similarity	NPC98777
0.7097	Intermediate Similarity	NPC260681
0.7015	Intermediate Similarity	NPC188555
0.6909	Remote Similarity	NPC12308
0.678	Remote Similarity	NPC26080
0.678	Remote Similarity	NPC165686
0.6774	Remote Similarity	NPC252169
0.6765	Remote Similarity	NPC138350
0.6765	Remote Similarity	NPC165482
0.6716	Remote Similarity	NPC130496
0.6667	Remote Similarity	NPC185778
0.6618	Remote Similarity	NPC40664
0.6618	Remote Similarity	NPC197723
0.6508	Remote Similarity	NPC65530
0.6338	Remote Similarity	NPC289346
0.6066	Remote Similarity	NPC479028
0.6066	Remote Similarity	NPC479031
0.6	Remote Similarity	NPC142319
0.5938	Remote Similarity	NPC59324
0.5909	Remote Similarity	NPC604095
0.5882	Remote Similarity	NPC57587
0.5875	Remote Similarity	NPC59692
0.5833	Remote Similarity	NPC238243
0.5769	Remote Similarity	NPC233467
0.5735	Remote Similarity	NPC189115
0.5696	Remote Similarity	NPC157396
0.5634	Remote Similarity	NPC88484
0.5606	Remote Similarity	NPC478871
0.5606	Remote Similarity	NPC478870
0.5606	Remote Similarity	NPC478872
0.5606	Remote Similarity	NPC478873
0.5556	Remote Similarity	NPC484946
0.5556	Remote Similarity	NPC484951
0.5556	Remote Similarity	NPC280606
0.5541	Remote Similarity	NPC168358
0.5526	Remote Similarity	NPC89686
0.5526	Remote Similarity	NPC257095
0.5513	Remote Similarity	NPC100936
0.5513	Remote Similarity	NPC1253
0.55	Remote Similarity	NPC23431
0.5405	Remote Similarity	NPC145319
0.5373	Remote Similarity	NPC478888
0.5362	Remote Similarity	NPC121001
0.5352	Remote Similarity	NPC606353
0.5303	Remote Similarity	NPC222455
0.5278	Remote Similarity	NPC186406
0.5246	Remote Similarity	NPC200092
0.5244	Remote Similarity	NPC478877
0.5238	Remote Similarity	NPC40377
0.5231	Remote Similarity	NPC210015
0.5231	Remote Similarity	NPC481303
0.5211	Remote Similarity	NPC259767
0.5211	Remote Similarity	NPC99233
0.5205	Remote Similarity	NPC185103
0.52	Remote Similarity	NPC166180
0.5172	Remote Similarity	NPC212729
0.5172	Remote Similarity	NPC604498
0.5167	Remote Similarity	NPC152722
0.5161	Remote Similarity	NPC145900
0.5152	Remote Similarity	NPC479029
0.5125	Remote Similarity	NPC152346
0.5125	Remote Similarity	NPC197703
0.5119	Remote Similarity	NPC478885
0.5085	Remote Similarity	NPC269242
0.5085	Remote Similarity	NPC484157
0.5082	Remote Similarity	NPC60589
0.5082	Remote Similarity	NPC469708
0.5079	Remote Similarity	NPC166168
0.5079	Remote Similarity	NPC214454
0.5077	Remote Similarity	NPC205054
0.5072	Remote Similarity	NPC469661
0.507	Remote Similarity	NPC475084
0.5067	Remote Similarity	NPC149244
0.5067	Remote Similarity	NPC3293

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC190429 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5342
0.1-0.2	3671
0.2-0.3	125
0.3-0.4	10
0.4-0.5	2
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