NPASS Compound

Natural Product: NPC274927

Natural Product ID	NPC274927
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(E)-8-Oxooctadec-9-Enoic Acid
IUPAC Name	(E)-8-oxooctadec-9-enoic acid
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL465675
PubChem CID	637456
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000504] Lineolic acids and derivatives

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 53 52 0 0 0 0 0 0 0 0999 V2000 -6.6937 1.8039 -0.5650 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7071 0.4818 -1.2633 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6176 -0.6922 -0.3500 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3834 -0.7460 0.4895 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1198 -0.8065 -0.2974 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8819 -0.8626 0.5615 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7485 0.3548 1.4497 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4716 0.2286 2.2799 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3753 0.1289 1.2519 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4155 -0.9201 1.1823 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4540 -0.9481 0.1578 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1697 -1.9725 0.1366 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5860 0.1901 -0.7536 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7273 0.2480 -1.6720 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0705 0.4669 -1.0971 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6302 -0.4597 -0.1022 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0591 -0.0226 0.2827 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9987 -0.0208 -0.8820 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3498 0.3852 -0.4261 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5906 1.5800 -0.1719 O 0 0 0 0 0 0 0 0 0 0 0 0 9.3379 -0.5587 -0.2837 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7721 2.1138 -0.4320 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2531 2.5832 -1.2338 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2547 1.7931 0.4475 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6520 0.3491 -1.8642 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8972 0.4576 -2.0282 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6212 -1.6074 -0.9961 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4904 -0.7904 0.3062 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3614 0.0368 1.2695 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4406 -1.7194 1.0630 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0650 0.1487 -0.8961 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1104 -1.6627 -0.9902 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8676 -1.7923 1.1773 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9570 -0.9045 -0.0466 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7434 1.2650 0.8292 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5776 0.3844 2.1778 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5232 -0.6401 2.9355 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3045 1.1461 2.8715 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2600 0.9425 0.5740 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2905 -1.7447 1.8781 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6034 0.3771 -1.3109 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6211 1.1362 -0.0966 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7270 -0.6123 -2.4161 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5285 1.1439 -2.3642 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7894 0.5402 -1.9864 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0392 1.5305 -0.6552 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0638 -0.4576 0.8615 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7300 -1.4781 -0.4565 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9314 0.9862 0.7307 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4100 -0.6806 1.1021 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7093 0.7184 -1.6727 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0885 -1.0362 -1.3414 H 0 0 0 0 0 0 0 0 0 0 0 0 10.2292 -0.3850 0.1444 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 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 2 0 11 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 2 0 19 21 1 0 1 22 1 0 1 23 1 0 1 24 1 0 2 25 1 0 2 26 1 0 3 27 1 0 3 28 1 0 4 29 1 0 4 30 1 0 5 31 1 0 5 32 1 0 6 33 1 0 6 34 1 0 7 35 1 0 7 36 1 0 8 37 1 0 8 38 1 0 9 39 1 0 10 40 1 0 13 41 1 0 13 42 1 0 14 43 1 0 14 44 1 0 15 45 1 0 15 46 1 0 16 47 1 0 16 48 1 0 17 49 1 0 17 50 1 0 18 51 1 0 18 52 1 0 21 53 1 0 M END

Standard InCHIKey	PHIXKQDGLSTYQU-SDNWHVSQSA-N
Standard InCHI	InChI=1S/C18H32O3/c1-2-3-4-5-6-7-8-11-14-17(19)15-12-9-10-13-16-18(20)21/h11,14H,2-10,12-13,15-16H2,1H3,(H,20,21)/b14-11+
SMILES	CCCCCCCC/C=C/C(=O)CCCCCCC(=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
NPO33018	clitocybe clavipes	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12444711]

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	1

Activity Type	# Activity
Individual protein	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT6555	Individual protein	Aldehyde dehydrogenase 1, mitochondrial	Saccharomyces cerevisiae	IC50	=	280000.0	nM	PMID[23228471]

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 NPC274927 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	32004
0.1-0.2	16188
0.2-0.3	1330
0.3-0.4	189
0.4-0.5	69
0.5-0.6	40
0.6-0.7	26
0.7-0.8	0
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC106851
1.0	High Similarity	NPC282788
0.8462	Intermediate Similarity	NPC251042
0.8462	Intermediate Similarity	NPC174447
0.8462	Intermediate Similarity	NPC122521
0.7838	Intermediate Similarity	NPC40082
0.75	Intermediate Similarity	NPC477201
0.6944	Remote Similarity	NPC424
0.6944	Remote Similarity	NPC36061
0.6944	Remote Similarity	NPC69510
0.6944	Remote Similarity	NPC77272
0.6944	Remote Similarity	NPC290563
0.6944	Remote Similarity	NPC139029
0.6944	Remote Similarity	NPC281972
0.6944	Remote Similarity	NPC261831
0.6944	Remote Similarity	NPC87564
0.6829	Remote Similarity	NPC482480
0.6829	Remote Similarity	NPC482481
0.6818	Remote Similarity	NPC235242
0.6757	Remote Similarity	NPC18712
0.6757	Remote Similarity	NPC74845
0.6757	Remote Similarity	NPC95145
0.6757	Remote Similarity	NPC325642
0.6757	Remote Similarity	NPC65174
0.6667	Remote Similarity	NPC281245
0.6486	Remote Similarity	NPC92114
0.6444	Remote Similarity	NPC325977
0.6444	Remote Similarity	NPC329550
0.641	Remote Similarity	NPC154245
0.641	Remote Similarity	NPC85813
0.641	Remote Similarity	NPC223697
0.641	Remote Similarity	NPC6095
0.6154	Remote Similarity	NPC321062
0.575	Remote Similarity	NPC5413
0.5745	Remote Similarity	NPC143396
0.5714	Remote Similarity	NPC171736
0.5714	Remote Similarity	NPC301585
0.5714	Remote Similarity	NPC261080
0.5714	Remote Similarity	NPC132565
0.5714	Remote Similarity	NPC209970
0.5714	Remote Similarity	NPC216630
0.5714	Remote Similarity	NPC201844
0.5714	Remote Similarity	NPC301696
0.5714	Remote Similarity	NPC196924
0.5714	Remote Similarity	NPC307783
0.5714	Remote Similarity	NPC154186
0.5714	Remote Similarity	NPC149184
0.5714	Remote Similarity	NPC279026
0.5714	Remote Similarity	NPC113928
0.5714	Remote Similarity	NPC14227
0.561	Remote Similarity	NPC52955
0.561	Remote Similarity	NPC88966
0.561	Remote Similarity	NPC25417
0.561	Remote Similarity	NPC1813
0.561	Remote Similarity	NPC59051
0.551	Remote Similarity	NPC322461
0.5435	Remote Similarity	NPC179764
0.5429	Remote Similarity	NPC155263
0.5366	Remote Similarity	NPC91495
0.5366	Remote Similarity	NPC70387
0.5319	Remote Similarity	NPC243532
0.5319	Remote Similarity	NPC255863
0.5319	Remote Similarity	NPC136164
0.5319	Remote Similarity	NPC245947
0.5263	Remote Similarity	NPC180534
0.5263	Remote Similarity	NPC611531
0.5208	Remote Similarity	NPC68343
0.5208	Remote Similarity	NPC318420
0.5208	Remote Similarity	NPC326268
0.5208	Remote Similarity	NPC328089
0.5111	Remote Similarity	NPC487561
0.5111	Remote Similarity	NPC225929
0.5111	Remote Similarity	NPC606120

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC274927 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5836
0.1-0.2	3073
0.2-0.3	193
0.3-0.4	28
0.4-0.5	9
0.5-0.6	8
0.6-0.7	3
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
0.6944	Remote Similarity	NPD3195	Phase 2
0.6944	Remote Similarity	NPD3196	Approved
0.641	Remote Similarity	NPD4266	Phase 2
0.5814	Remote Similarity	NPD3194	Phase 4
0.575	Remote Similarity	NPD3173	Phase 4
0.5714	Remote Similarity	NPD2270	Pre-clinical
0.5714	Remote Similarity	NPD633	Phase 3
0.5714	Remote Similarity	NPD9448	Phase 2
0.561	Remote Similarity	NPD3172	Approved
0.5263	Remote Similarity	NPD622	Pre-clinical
0.5208	Remote Similarity	NPD39	Phase 4

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