NPASS Compound

Natural Product: NPC608360

Natural Product ID	NPC608360
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	CDSSYLTXYXEANW-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL308688
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 35 37 0 0 0 0 0 0 0 0999 V2000 -5.5842 1.4071 0.0674 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8329 0.2205 0.1839 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4659 0.1572 0.1342 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8806 -1.0967 0.2660 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5208 -1.2907 0.2329 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9885 -2.5587 0.3687 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8310 -3.6652 0.5423 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6820 -0.1983 0.0612 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7048 -0.3832 0.0259 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2202 -1.5019 0.1437 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4914 0.7354 -0.1469 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9462 0.6333 -0.1955 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7726 1.4966 0.4908 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1449 1.3919 0.4385 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7604 0.4106 -0.3091 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9520 -0.4637 -1.0035 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5792 -0.3534 -0.9468 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8703 1.9496 -0.2722 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4496 2.0769 -0.2325 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2473 1.0586 -0.0718 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6251 1.2251 -0.0345 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5968 1.2826 0.5010 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1059 2.2706 0.5909 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6784 1.6472 -1.0093 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4984 -1.9839 0.4027 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3833 -3.8004 -0.4297 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2575 -4.5834 0.7500 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5659 -3.5238 1.3679 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3302 2.2783 1.0873 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7735 2.0955 0.9968 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8483 0.3201 -0.3564 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4253 -1.2339 -1.5904 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9507 -1.0586 -1.5064 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4805 2.8306 -0.4079 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0565 2.2081 -0.1390 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 5 8 2 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 11 18 2 0 18 19 1 0 19 20 1 0 20 21 2 0 21 3 1 0 20 8 1 0 17 12 1 0 1 22 1 0 1 23 1 0 1 24 1 0 4 25 1 0 7 26 1 0 7 27 1 0 7 28 1 0 13 29 1 0 14 30 1 0 15 31 1 0 16 32 1 0 17 33 1 0 18 34 1 0 21 35 1 0 M END

Standard InCHIKey	CDSSYLTXYXEANW-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C17H14O4/c1-19-12-8-14(20-2)16-15(9-12)21-10-13(17(16)18)11-6-4-3-5-7-11/h3-10H,1-2H3
SMILES	COc1cc(OC)c2c(=O)c(-c3ccccc3)coc2c1

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
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	n.a.	n.a.	2007; 2008	DOI[10.1007/s11746-010-1589-7]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	n.a.	cotyledon	n.a.	PMID[11283027]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	n.a.	seed	n.a.	PMID[12670184]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	n.a.	seed	n.a.	PMID[21348467]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[22537213]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	Peanut Skins	n.a.	n.a.	PMID[28231711]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[36431807]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	Leaf	n.a.	n.a.	Database[FooDB]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	n.a.	n.a.		Database[FooDB]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	Seed	n.a.	n.a.	Database[FooDB]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	Oil	n.a.	n.a.	Database[FooDB]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.		n.a.	n.a.	Database[FooDB]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	Oils	n.a.		Database[Phenol-Explorer]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	Seeds	n.a.		Database[Phenol-Explorer]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25426	Arachis hypogaea	Species	n.a.	n.a.	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
Potency	18
Inhibition	2
Rhodamine-123 accumulation	4

Activity Type	# Activity
Individual protein	16
Cell line	4
Unchecked	4

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT149	Individual protein	Endoplasmic reticulum-associated amyloid beta-peptide-binding protein	Homo sapiens	Potency	=	25118.9	nM	PubChem BioAssay data set
NPT109	Individual protein	Cytochrome P450 3A4	Homo sapiens	Potency	=	15848.9	nM	PubChem BioAssay data set
NPT151	Individual protein	15-hydroxyprostaglandin dehydrogenase [NAD+]	Homo sapiens	Potency	=	28183.8	nM	PubChem BioAssay data set
NPT72	Individual protein	Solute carrier organic anion transporter family member 1B3	Homo sapiens	Inhibition	=	104.71	%	PMID[23571415]
NPT50	Individual protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	6513.1	nM	PubChem BioAssay data set
NPT50	Individual protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	20596.2	nM	PubChem BioAssay data set
NPT48	Individual protein	Lysine-specific demethylase 4D-like	Homo sapiens	Potency	=	31622.8	nM	PubChem BioAssay data set
NPT73	Individual protein	Solute carrier organic anion transporter family member 1B1	Homo sapiens	Inhibition	=	99.46	%	PMID[23571415]
NPT94	Individual protein	Aldehyde dehydrogenase 1A1	Homo sapiens	Potency	=	19952.6	nM	PubChem BioAssay data set
NPT93	Individual protein	Survival motor neuron protein	Homo sapiens	Potency	=	11220.2	nM	PubChem BioAssay data set
NPT51	Individual protein	Microtubule-associated protein tau	Homo sapiens	Potency	=	1258.9	nM	PubChem BioAssay data set
NPT46	Individual protein	Thyroid hormone receptor beta-1	Homo sapiens	Potency	=	112201.8	nM	PubChem BioAssay data set
NPT539	Individual protein	Cellular tumor antigen p53	Homo sapiens	Potency	=	15848.9	nM	PubChem BioAssay data set
NPT539	Individual protein	Cellular tumor antigen p53	Homo sapiens	Potency	=	10000.0	nM	PubChem BioAssay data set
NPT53	Individual protein	4'-phosphopantetheinyl transferase ffp	Bacillus subtilis	Potency	=	79432.8	nM	PubChem BioAssay data set

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT111	Cell line	K562	Homo sapiens	Rhodamine-123 accumulation	=	40.0	arbitrary units	PMID[12747785]
NPT111	Cell line	K562	Homo sapiens	Rhodamine-123 accumulation	=	46.0	arbitrary units	PMID[12747785]
NPT111	Cell line	K562	Homo sapiens	Rhodamine-123 accumulation	=	54.0	arbitrary units	PMID[12747785]
NPT111	Cell line	K562	Homo sapiens	Rhodamine-123 accumulation	=	49.0	arbitrary units	PMID[12747785]
NPT28438	Unchecked	Unchecked	n.a.	Potency	n.a.	1122.0	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	Potency	n.a.	1258.9	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	Potency	=	3548.1	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	Potency	=	5011.9	nM	PubChem BioAssay data set

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 NPC608360 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	35199
0.1-0.2	12795
0.2-0.3	1516
0.3-0.4	250
0.4-0.5	77
0.5-0.6	13
0.6-0.7	1
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
0.8298	Intermediate Similarity	NPC223354
0.7647	Intermediate Similarity	NPC162680
0.6	Remote Similarity	NPC1820
0.5968	Remote Similarity	NPC476054
0.5645	Remote Similarity	NPC474999
0.5614	Remote Similarity	NPC479067
0.5455	Remote Similarity	NPC182428
0.5345	Remote Similarity	NPC7013
0.5278	Remote Similarity	NPC100720
0.5273	Remote Similarity	NPC61546
0.5246	Remote Similarity	NPC220050
0.5179	Remote Similarity	NPC120924
0.5179	Remote Similarity	NPC278556
0.5167	Remote Similarity	NPC283429
0.5085	Remote Similarity	NPC116632
0.5085	Remote Similarity	NPC603503

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC608360 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5297
0.1-0.2	3754
0.2-0.3	95
0.3-0.4	3
0.4-0.5	0
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
0.5614	Remote Similarity	NPD2796	Phase 2

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