NPASS Compound

Natural Product: NPC162939

Natural Product ID	NPC162939
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	6-[(3E,5E,7S)-5,7-Dimethyl-2-Oxonona-3,5-Dienyl]-2,4-Dihydroxy-3-Methylbenzaldehyde
IUPAC Name	6-[(3E,5E,7S)-5,7-dimethyl-2-oxonona-3,5-dienyl]-2,4-dihydroxy-3-methylbenzaldehyde
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1456313
PubChem CID	16745396
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0001831] Carbonyl compounds [CHEMONTID:0000124] Aldehydes [CHEMONTID:0003213] Aryl-aldehydes [CHEMONTID:0001345] Benzaldehydes [CHEMONTID:0003978] Hydroxybenzaldehydes

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 47 47 0 0 0 0 0 0 0 0999 V2000 -7.1034 1.0139 1.2370 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7776 0.3836 0.7029 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8953 1.5067 0.3020 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.4880 2.3645 -0.8048 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4622 1.3585 0.2761 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7525 0.2748 0.1379 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4087 -1.0334 -0.0263 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2711 0.3516 0.1537 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4593 -0.6621 0.0368 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0098 -0.4811 0.0625 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4442 0.6834 0.1915 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9312 -1.6044 -0.0559 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3516 -1.2056 -0.0322 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0789 -1.3817 1.1207 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4146 -1.0197 1.2149 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0567 -0.4624 0.1287 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4846 -0.0538 0.1637 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3166 -0.2896 -1.0260 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9790 -0.6500 -1.1266 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2880 -0.4327 -2.3903 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2690 -1.3130 -3.2933 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9256 0.2610 -2.1221 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0999 -1.2200 2.4033 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8752 1.7699 1.9893 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6115 1.4291 0.3523 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7020 0.1617 1.5916 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1799 -0.1926 -0.1828 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4146 -0.2359 1.5136 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0392 2.2445 1.2279 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7293 2.5133 -1.6293 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4224 1.9129 -1.2224 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7606 3.3840 -0.4817 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8276 2.2873 0.3876 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6494 -1.7004 -0.5593 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2299 -1.0207 -0.7723 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6112 -1.5800 0.9001 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7989 1.3243 0.2698 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8387 -1.6522 -0.0725 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7871 -2.3642 0.7684 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7825 -2.2063 -0.9845 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6394 -1.8162 2.0225 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6658 0.6926 -0.6327 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7728 0.3051 1.1510 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0604 -0.9777 -0.1388 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7880 0.5082 -2.5372 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2015 -0.3754 -2.8716 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9613 -0.7998 2.6569 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 3 5 1 0 5 6 2 0 6 7 1 0 6 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 10 12 1 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 16 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 18 22 1 0 15 23 1 0 19 13 1 0 1 24 1 0 1 25 1 0 1 26 1 0 2 27 1 0 2 28 1 0 3 29 1 1 4 30 1 0 4 31 1 0 4 32 1 0 5 33 1 0 7 34 1 0 7 35 1 0 7 36 1 0 8 37 1 0 9 38 1 0 12 39 1 0 12 40 1 0 14 41 1 0 17 42 1 0 17 43 1 0 17 44 1 0 20 45 1 0 22 46 1 0 23 47 1 0 M END

Standard InCHIKey	SRUILBLGVMJFPG-YDROHTJRSA-N
Standard InCHI	InChI=1S/C19H24O4/c1-5-12(2)8-13(3)6-7-16(21)9-15-10-18(22)14(4)19(23)17(15)11-20/h6-8,10-12,22-23H,5,9H2,1-4H3/b7-6+,13-8+/t12-/m0/s1
SMILES	CC[C@H](C)/C=C(C)/C=C/C(=O)Cc1cc(c(C)c(c1C=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
NPO14633	Tridacna maxima	Species	Tridacnidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9160	Plantago nivalis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13628	Rabdosia longituba	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15729	Streptomyces karnatakensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3508	Aglaia tenuicaulis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13628	Rabdosia longituba	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13628	Rabdosia longituba	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5308	Stilpnopappus trichospiroides	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO9160	Plantago nivalis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14633	Tridacna maxima	Species	Tridacnidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20456	Chrysanthemum tatsienense	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3508	Aglaia tenuicaulis	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16003	Machaerium incorruptibile	Species	Dolichopodidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7875	Pseudocyphellaria berberina	Species	Lobariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15729	Streptomyces karnatakensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO10933	Stenanthera gabonensis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO13628	Rabdosia longituba	Species	Lamiaceae	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
Potency	22
EC50	1

Activity Type	# Activity
Individual protein	19
Organism	2
Protein-protein interaction	1
Others	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT3	Individual protein	Thioredoxin glutathione reductase	Schistosoma mansoni	Potency	=	28183.8	nM	PubChem BioAssay data set
NPT1415	Individual protein	Heat shock factor protein 1	Mus musculus	EC50	=	27470.0	nM	PubChem BioAssay data set
NPT10	Individual protein	Geminin	Homo sapiens	Potency	n.a.	25929.0	nM	PubChem BioAssay data set
NPT101	Individual protein	Glucagon-like peptide 1 receptor	Homo sapiens	Potency	n.a.	10000.0	nM	PubChem BioAssay data set
NPT11	Individual protein	Guanine nucleotide-binding protein G(s), subunit alpha	Homo sapiens	Potency	n.a.	31622.8	nM	PubChem BioAssay data set
NPT9	Individual protein	DNA polymerase eta	Homo sapiens	Potency	n.a.	50118.7	nM	PubChem BioAssay data set
NPT48	Individual protein	Lysine-specific demethylase 4D-like	Homo sapiens	Potency	=	31622.8	nM	PubChem BioAssay data set
NPT7	Individual protein	Thioredoxin reductase 1, cytoplasmic	Rattus norvegicus	Potency	n.a.	70794.6	nM	PubChem BioAssay data set
NPT444	Individual protein	Ubiquitin carboxyl-terminal hydrolase 1	Homo sapiens	Potency	n.a.	35481.3	nM	PubChem BioAssay data set
NPT446	Individual protein	Rap guanine nucleotide exchange factor 3	Homo sapiens	Potency	n.a.	70794.6	nM	PubChem BioAssay data set
NPT51	Individual protein	Microtubule-associated protein tau	Homo sapiens	Potency	=	35481.3	nM	PubChem BioAssay data set
NPT51	Individual protein	Microtubule-associated protein tau	Homo sapiens	Potency	=	39810.7	nM	PubChem BioAssay data set
NPT59	Individual protein	DNA polymerase beta	Homo sapiens	Potency	=	35481.3	nM	PubChem BioAssay data set
NPT63	Individual protein	Bromodomain adjacent to zinc finger domain protein 2B	Homo sapiens	Potency	n.a.	79432.8	nM	PubChem BioAssay data set
NPT8	Individual protein	DNA polymerase iota	Homo sapiens	Potency	n.a.	15848.9	nM	PubChem BioAssay data set
NPT755	Individual protein	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	Homo sapiens	Potency	n.a.	56234.1	nM	PubChem BioAssay data set
NPT197	Protein-protein interaction	Menin/Histone-lysine N-methyltransferase MLL	Homo sapiens	Potency	=	28183.8	nM	PubChem BioAssay data set
NPT53	Individual protein	4'-phosphopantetheinyl transferase ffp	Bacillus subtilis	Potency	=	89125.1	nM	PubChem BioAssay data set
NPT532	Individual protein	Lysine-specific demethylase 4A	Homo sapiens	Potency	n.a.	22387.2	nM	PubChem BioAssay data set
NPT5	Individual protein	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3	Homo sapiens	Potency	n.a.	794.3	nM	PubChem BioAssay data set

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	8275.3	nM	PubChem BioAssay data set
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	13115.4	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	31622.8	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 NPC162939 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	11189
0.1-0.2	36354
0.2-0.3	2285
0.3-0.4	27
0.4-0.5	1
0.5-0.6	1
0.6-0.7	1
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
0.6087	Remote Similarity	NPC474519
0.5273	Remote Similarity	NPC606876

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC162939 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3724
0.1-0.2	5373
0.2-0.3	53
0.3-0.4	0
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