NPASS Compound

Natural Product: NPC152659

Natural Product ID	NPC152659
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	LERNWSHUQATAEP-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3421659
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones [CHEMONTID:0003517] 2-prenylated xanthones

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 56 59 0 0 0 0 0 0 0 0999 V2000 6.4053 1.2727 1.8636 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5505 0.0953 1.4933 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1068 -0.0429 0.2580 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2597 -1.1746 -0.1808 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9914 -0.6242 -0.7464 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0192 -0.0518 -2.0030 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8577 0.4538 -2.5197 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6793 0.3981 -1.8089 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6483 -0.1747 -0.5505 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8209 -0.6797 -0.0411 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7526 -1.2523 1.2337 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5222 -0.2489 0.1973 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5521 -0.7647 1.3316 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6616 0.2780 -0.3746 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9085 0.2747 0.2593 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9711 -0.3288 1.5905 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3421 -0.3408 2.2271 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4516 -0.1977 1.2257 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7057 -1.5025 0.5036 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7669 0.1691 1.9235 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2162 0.7993 0.2841 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9949 0.8213 -0.3797 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8933 1.3822 -1.6479 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6820 1.3979 -2.2912 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5963 0.8481 -1.6443 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4399 0.8786 -2.2904 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0271 1.9202 -2.2450 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2131 0.0074 -2.7292 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2664 0.5861 -4.0118 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2005 -0.9379 2.5066 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7445 2.1587 1.9614 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8372 1.0704 2.8620 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2211 1.4404 1.1593 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3733 0.7079 -0.4733 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0620 -1.8895 0.6309 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7585 -1.7151 -1.0382 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8695 0.8999 -3.4940 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8764 -2.2764 1.2326 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3327 0.2270 2.3353 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6994 -1.4291 1.5577 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4718 0.5085 2.9567 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5463 -1.2541 2.8254 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8041 -2.1234 0.3894 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1416 -1.3425 -0.5165 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4573 -2.1179 1.0724 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0883 -0.6076 2.6152 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5415 0.3230 1.1473 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5831 1.1589 2.3966 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6112 1.8372 -3.2799 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8950 2.5159 -3.0497 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8027 -0.0641 -4.7883 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3286 0.7003 -4.3126 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7894 1.5915 -4.0157 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1355 -1.1803 2.5357 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5075 -0.5383 3.4982 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8256 -1.8629 2.3586 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 3 3 4 1 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 9 12 1 0 12 13 2 0 12 14 1 0 14 15 2 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 18 20 1 0 18 21 1 0 21 22 1 0 22 23 2 0 23 24 1 0 24 25 2 0 25 26 1 0 23 27 1 0 6 28 1 0 28 29 1 0 2 30 1 0 10 5 1 0 25 14 1 0 26 8 1 0 22 15 1 0 1 31 1 0 1 32 1 0 1 33 1 0 3 34 1 0 4 35 1 0 4 36 1 0 7 37 1 0 11 38 1 0 16 39 1 0 16 40 1 0 17 41 1 0 17 42 1 0 19 43 1 0 19 44 1 0 19 45 1 0 20 46 1 0 20 47 1 0 20 48 1 0 24 49 1 0 27 50 1 0 29 51 1 0 29 52 1 0 29 53 1 0 30 54 1 0 30 55 1 0 30 56 1 0 M END

Standard InCHIKey	LERNWSHUQATAEP-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C24H26O6/c1-12(2)6-7-13-16(28-5)11-18-20(21(13)26)22(27)19-14-8-9-24(3,4)30-23(14)15(25)10-17(19)29-18/h6,10-11,25-26H,7-9H2,1-5H3
SMILES	CC(=CCc1c(cc2c(c1O)c(=O)c1c3CCC(C)(C)Oc3c(cc1o2)O)OC)C

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
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1071/CH03175]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	twigs	n.a.	n.a.	PMID[20058933]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	young fruits	Khokkhon, Tha Bo District, Nong Khai Province, Thailand	2011-Aug	PMID[25651042]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	flowers	Pakook, Muang District, Chiang Rai Province, Thailand	2013-Feb	PMID[25651042]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[31860303]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25472	Garcinia cowa	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25472	Garcinia cowa	Species	Clusiaceae	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
MIC	5
Inhibition	1

Activity Type	# Activity
Organism	5
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
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	MIC	=	128.0	ug.mL-1	PMID[15217297]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	128.0	ug.mL-1	PMID[22122518]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	128.0	ug.mL-1	PMID[12880317]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	>	128.0	ug.mL-1	PMID[11908979]
NPT314	Organism	Bacillus cereus	Bacillus cereus	MIC	=	128.0	ug.mL-1	PMID[15165146]
NPT2	Others	Unspecified	n.a.	Inhibition	>	100.0	%	PMID[10650083]

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 NPC152659 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	20046
0.1-0.2	25129
0.2-0.3	4254
0.3-0.4	337
0.4-0.5	45
0.5-0.6	28
0.6-0.7	10
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
0.7971	Intermediate Similarity	NPC236521
0.7879	Intermediate Similarity	NPC146134
0.7846	Intermediate Similarity	NPC14353
0.7429	Intermediate Similarity	NPC25152
0.726	Intermediate Similarity	NPC239752
0.6986	Remote Similarity	NPC210446
0.6714	Remote Similarity	NPC604618
0.6667	Remote Similarity	NPC117854
0.6429	Remote Similarity	NPC165977
0.6338	Remote Similarity	NPC200746
0.6316	Remote Similarity	NPC275780
0.6234	Remote Similarity	NPC170245
0.6184	Remote Similarity	NPC248638
0.6111	Remote Similarity	NPC56085
0.6098	Remote Similarity	NPC472449
0.5974	Remote Similarity	NPC310349
0.5974	Remote Similarity	NPC61010
0.589	Remote Similarity	NPC228785
0.5867	Remote Similarity	NPC474186
0.5867	Remote Similarity	NPC475886
0.5833	Remote Similarity	NPC39091
0.5769	Remote Similarity	NPC474287
0.5769	Remote Similarity	NPC475883
0.5714	Remote Similarity	NPC474350
0.5676	Remote Similarity	NPC266499
0.5625	Remote Similarity	NPC474351
0.557	Remote Similarity	NPC474187
0.5556	Remote Similarity	NPC40491
0.5556	Remote Similarity	NPC278052
0.5541	Remote Similarity	NPC241904
0.5395	Remote Similarity	NPC152951
0.5352	Remote Similarity	NPC174999
0.5244	Remote Similarity	NPC6588
0.5185	Remote Similarity	NPC189473
0.5185	Remote Similarity	NPC229632
0.5169	Remote Similarity	NPC150977
0.5128	Remote Similarity	NPC479160
0.5122	Remote Similarity	NPC300727
0.5114	Remote Similarity	NPC479159
0.5065	Remote Similarity	NPC479167
0.5057	Remote Similarity	NPC7483
0.5057	Remote Similarity	NPC479157
0.5057	Remote Similarity	NPC74766

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC152659 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3178
0.1-0.2	5884
0.2-0.3	87
0.3-0.4	1
0.4-0.5	0
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