NPASS Compound

Natural Product: NPC479029

Natural Product ID	NPC479029
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	KWKARGHAJCHTBH-JMQKIHFDSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	10457775
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 -2.6435 4.5836 2.1373 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3872 3.3315 1.5450 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2600 2.6295 1.9460 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4135 3.1753 2.9192 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7138 2.5469 3.3648 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1015 1.2896 2.8645 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2084 0.6218 3.4824 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0362 -0.1852 2.9312 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0561 -0.5769 1.5613 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5226 -1.8488 1.2517 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7296 -2.2915 -0.0286 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4687 -1.4473 -1.0991 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0065 -0.1821 -0.8090 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7997 0.2591 0.5063 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7352 0.6888 -1.8538 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2547 2.0141 -1.6097 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6752 -1.8875 -2.4000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7227 -2.5221 -3.1948 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1956 -3.5634 -0.3218 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4653 -4.4322 0.7606 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2628 0.7747 1.9199 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9019 1.4002 1.4433 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6530 0.7789 0.4938 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7817 1.0007 -0.2031 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5651 1.1262 -1.7137 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.6317 0.3581 -2.4576 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5580 -1.1177 -2.0857 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5721 -1.1648 -0.5763 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3701 -1.9150 -0.1144 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3473 -3.1317 -0.8183 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7947 0.0522 -0.0071 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6825 -1.7301 -2.6527 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4448 0.4368 -3.8245 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6475 2.4456 -2.1385 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7097 4.4173 3.2486 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5806 5.0440 1.7568 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7828 5.2700 1.9944 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6916 4.1557 3.3276 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3620 2.9742 4.1148 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3874 0.8162 4.5770 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8457 -0.6389 3.6068 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7457 -2.5596 2.0574 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4796 1.2877 0.6042 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2871 1.9940 -1.0799 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0370 2.5567 -1.0040 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1771 2.5703 -2.5640 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4370 -3.4822 -2.7367 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2470 -2.7879 -4.1580 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8345 -1.8779 -3.4130 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9373 -5.3819 0.4331 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4816 -4.6336 1.2570 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1118 -3.9794 1.5332 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4438 -0.2218 1.5110 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2661 1.9660 0.0798 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5733 0.6722 -1.9607 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6273 0.7888 -2.2122 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6282 -1.5193 -2.5075 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4645 -1.8040 -0.3059 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4151 -1.3611 -0.3388 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4013 -2.1494 0.9540 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9978 -3.7229 -0.3459 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5202 -1.3086 -2.3465 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4273 -0.4411 -4.2685 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0292 2.5430 -3.0328 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 9 10 2 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 13 15 1 0 15 16 1 0 12 17 1 0 17 18 1 0 11 19 1 0 19 20 1 0 6 21 1 0 21 22 2 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 28 29 1 0 29 30 1 0 28 31 1 0 27 32 1 0 26 33 1 0 25 34 1 0 22 3 1 0 31 24 1 0 14 9 1 0 1 35 1 0 1 36 1 0 1 37 1 0 4 38 1 0 5 39 1 0 7 40 1 0 8 41 1 0 10 42 1 0 14 43 1 0 16 44 1 0 16 45 1 0 16 46 1 0 18 47 1 0 18 48 1 0 18 49 1 0 20 50 1 0 20 51 1 0 20 52 1 0 21 53 1 0 24 54 1 1 25 55 1 1 26 56 1 6 27 57 1 6 28 58 1 6 29 59 1 0 29 60 1 0 30 61 1 0 32 62 1 0 33 63 1 0 34 64 1 0 M END

Standard InCHIKey	KWKARGHAJCHTBH-JMQKIHFDSA-N
Standard InCHI	InChI=1S/C24H30O10/c1-29-15-8-7-13(5-6-14-10-17(30-2)23(32-4)18(11-14)31-3)9-16(15)33-24-22(28)21(27)20(26)19(12-25)34-24/h5-11,19-22,24-28H,12H2,1-4H3/b6-5-/t19-,20-,21+,22-,24-/m1/s1
SMILES	COc1ccc(/C=Cc2cc(c(c(c2)OC)OC)OC)cc1O[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
NPO20665	Erythrophleum lasianthum	Species	Fabaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[9392877]
NPO20665	Erythrophleum lasianthum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20665	Erythrophleum lasianthum	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

Activity Type	# Activity
IC50	9
Ratio	2
Ratio IC50	1

Activity Type	# Activity
Individual protein	6
Cell line	4
Organism	1
Others	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1540	Individual protein	Solute carrier family 22 member 2	Homo sapiens	IC50	>	200000.0	nM	PMID[30108866]
NPT613	Individual protein	Solute carrier family 22 member 1	Homo sapiens	IC50	>	200000.0	nM	PMID[30108866]
NPT72	Individual protein	Solute carrier organic anion transporter family member 1B3	Homo sapiens	IC50	>	200000.0	nM	PMID[30108866]
NPT669	Individual protein	Solute carrier family 22 member 8	Homo sapiens	IC50	>	200000.0	nM	PMID[30108866]
NPT665	Individual protein	Solute carrier family 22 member 6	Homo sapiens	IC50	>	200000.0	nM	PMID[30108866]
NPT622	Individual protein	Solute carrier organic anion transporter family member 2B1	Homo sapiens	IC50	>	200000.0	nM	PMID[30108866]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT139	Cell line	HT-29	Homo sapiens	IC50	=	6910.0	nM	PMID[30108866]
NPT139	Cell line	HT-29	Homo sapiens	Ratio IC50	=	9.59	n.a.	PMID[30108866]
NPT20967	Cell line	Platelet	n.a.	IC50	=	300.0	ug	PMID[9392877]
NPT35	Others	n.a.	n.a.	Ratio	=	610.0	n.a.	PMID[30108866]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT32	Organism	Mus musculus	Mus musculus	Ratio	=	16.0	n.a.	PMID[30108866]

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 NPC479029 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	16424
0.1-0.2	28432
0.2-0.3	3938
0.3-0.4	702
0.4-0.5	266
0.5-0.6	67
0.6-0.7	14
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	Natural Product ID
0.7167	Intermediate Similarity	NPC479030
0.7167	Intermediate Similarity	NPC604095
0.6935	Remote Similarity	NPC475084
0.6897	Remote Similarity	NPC248355
0.6842	Remote Similarity	NPC479028
0.6842	Remote Similarity	NPC479031
0.678	Remote Similarity	NPC55040
0.6667	Remote Similarity	NPC302378
0.6441	Remote Similarity	NPC210478
0.6379	Remote Similarity	NPC49074
0.6349	Remote Similarity	NPC37468
0.6316	Remote Similarity	NPC166040
0.6271	Remote Similarity	NPC162093
0.6071	Remote Similarity	NPC299144
0.6	Remote Similarity	NPC472024
0.6	Remote Similarity	NPC270849
0.5938	Remote Similarity	NPC294166
0.5938	Remote Similarity	NPC115022
0.5932	Remote Similarity	NPC9912
0.5926	Remote Similarity	NPC276195
0.5902	Remote Similarity	NPC26653
0.5902	Remote Similarity	NPC80600
0.5873	Remote Similarity	NPC232673
0.5862	Remote Similarity	NPC69513
0.5846	Remote Similarity	NPC246947
0.5781	Remote Similarity	NPC470236
0.5769	Remote Similarity	NPC228907
0.5763	Remote Similarity	NPC48863
0.5763	Remote Similarity	NPC251981
0.5763	Remote Similarity	NPC13745
0.5738	Remote Similarity	NPC604356
0.5714	Remote Similarity	NPC153149
0.5692	Remote Similarity	NPC276753
0.5692	Remote Similarity	NPC205796
0.569	Remote Similarity	NPC200092
0.5672	Remote Similarity	NPC98777
0.5667	Remote Similarity	NPC215833
0.5645	Remote Similarity	NPC214910
0.5645	Remote Similarity	NPC26080
0.5645	Remote Similarity	NPC165686
0.5614	Remote Similarity	NPC25817
0.5541	Remote Similarity	NPC93924
0.5536	Remote Similarity	NPC217854
0.5507	Remote Similarity	NPC148273
0.5469	Remote Similarity	NPC95392
0.5469	Remote Similarity	NPC84013
0.5469	Remote Similarity	NPC55715
0.5469	Remote Similarity	NPC35877
0.5441	Remote Similarity	NPC212770
0.5441	Remote Similarity	NPC475096
0.5424	Remote Similarity	NPC608788
0.5385	Remote Similarity	NPC59324
0.5373	Remote Similarity	NPC486107
0.5357	Remote Similarity	NPC212729
0.5357	Remote Similarity	NPC604498
0.5352	Remote Similarity	NPC158635
0.5352	Remote Similarity	NPC229882
0.5345	Remote Similarity	NPC152722
0.5323	Remote Similarity	NPC218685
0.5303	Remote Similarity	NPC100389
0.5286	Remote Similarity	NPC486102
0.5263	Remote Similarity	NPC269242
0.5254	Remote Similarity	NPC609376
0.5238	Remote Similarity	NPC251102
0.5238	Remote Similarity	NPC210298
0.5231	Remote Similarity	NPC104167
0.5224	Remote Similarity	NPC65530
0.5172	Remote Similarity	NPC294470
0.5167	Remote Similarity	NPC226712
0.5156	Remote Similarity	NPC481303
0.5152	Remote Similarity	NPC85799
0.5152	Remote Similarity	NPC303422
0.5152	Remote Similarity	NPC218003
0.5147	Remote Similarity	NPC8497
0.5143	Remote Similarity	NPC295970
0.5125	Remote Similarity	NPC478985
0.5072	Remote Similarity	NPC260681
0.5072	Remote Similarity	NPC146803
0.5072	Remote Similarity	NPC164857
0.507	Remote Similarity	NPC486104
0.5068	Remote Similarity	NPC61594
0.5068	Remote Similarity	NPC286235
0.5065	Remote Similarity	NPC43508

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC479029 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4380
0.1-0.2	4576
0.2-0.3	176
0.3-0.4	13
0.4-0.5	4
0.5-0.6	1
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
0.5167	Remote Similarity	NPD1091	Pre-clinical

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