NPASS Compound

Natural Product: NPC542578

Natural Product ID	NPC542578
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ethyl hexadeca-10,13-dienoate
IUPAC Name	ethyl hexadeca-10,13-dienoate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
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 52 51 0 0 0 0 0 0 0 0999 V2000 6.6026 1.4068 -0.7572 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1384 0.9766 -0.7929 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2832 1.8937 -0.0260 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5328 1.7005 1.0210 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2518 0.5213 1.8366 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9635 -0.7007 1.4780 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4213 -1.8178 1.0835 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9735 -2.0614 0.9222 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6261 -2.4403 -0.5028 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1682 -2.7119 -0.6466 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6658 -1.4975 -0.2653 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3245 -0.3322 -1.1112 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9849 0.9601 -0.9198 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3992 1.2099 -1.1216 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4001 0.4881 -0.3189 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8077 0.9967 -0.6544 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9572 1.9008 -1.5081 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9271 0.4860 -0.0406 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2416 0.9282 -0.3223 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1694 0.1082 0.5681 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2032 0.5415 -1.1457 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8856 1.6978 0.2658 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7827 2.2659 -1.4226 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9678 -0.0731 -0.5898 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8233 1.0756 -1.9067 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2850 2.9554 -0.4262 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9666 2.6211 1.4031 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4773 0.7846 2.9475 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1301 0.3962 1.8727 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0837 -0.7249 1.5686 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1171 -2.6524 0.8505 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3976 -1.1706 1.1698 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6730 -2.9457 1.5475 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0218 -1.6772 -1.2007 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2329 -3.3718 -0.7709 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1383 -3.5620 0.0185 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0913 -3.0574 -1.6768 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7489 -1.7906 -0.3178 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5023 -1.3180 0.8217 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4069 -0.6032 -2.2120 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8058 -0.1656 -0.9817 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6646 1.4364 0.0831 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4309 1.6940 -1.6306 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6582 1.0065 -2.2162 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5801 2.3315 -0.9750 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2901 0.5464 0.7743 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4611 -0.5822 -0.6250 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5112 0.7520 -1.3897 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3700 2.0137 -0.1483 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.2285 0.3756 0.4292 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0312 -0.9586 0.2319 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8238 0.1438 1.6081 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 3 4 5 1 0 5 6 1 0 6 7 2 3 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 2 0 16 18 1 0 18 19 1 0 19 20 1 0 1 21 1 0 1 22 1 0 1 23 1 0 2 24 1 0 2 25 1 0 3 26 1 0 4 27 1 0 5 28 1 0 5 29 1 0 6 30 1 0 7 31 1 0 8 32 1 0 8 33 1 0 9 34 1 0 9 35 1 0 10 36 1 0 10 37 1 0 11 38 1 0 11 39 1 0 12 40 1 0 12 41 1 0 13 42 1 0 13 43 1 0 14 44 1 0 14 45 1 0 15 46 1 0 15 47 1 0 19 48 1 0 19 49 1 0 20 50 1 0 20 51 1 0 20 52 1 0 M END

Standard InCHIKey	NSOPDUMLFDNMEX-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C18H32O2/c1-3-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20-4-2/h5-6,8-9H,3-4,7,10-17H2,1-2H3
SMILES	CCC=CCC=CCCCCCCCCC(=O)OCC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	280.24	Volume:	329.555 ? Van der Waals volume.
Dense:	0.85	LogP:	6.23 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.804 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-6.0 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	14.0	Rigid Bonds:	3.0
TPSA:	26.3 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	0.0	Rings:	0.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.25	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.339	Fsp³:	0.722
MCE-18:	0.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.074	Fluc inhibitor:	0.066 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.003 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.009 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.997	Promiscuous compounds:	0.314

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.948	MDCK Permeability:	-4.695
Pgp-inhibitor:	0.454	Pgp-substrate:	0.009
PAMPA:	0.004 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.623	30% Bioavailability (F30%):	0.764
50% Bioavailability (F50%):	0.894

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.053	MRP1:	0.993
Plasma Protein Binding (PPB):	98.113%	Volume Distribution (VD):	-0.448
Fu:	1.522% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.113
OATP1B3 inhibitor:	0.982	BCRP inhibitor:	0.268
BSEP inhibitor:	0.999

ADMET: Metabolism

CYP1A2-inhibitor:	0.001	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.013	CYP2C19-substrate:	0.836
CYP2C9-inhibitor:	0.846	CYP2C9-substrate:	0.001
CYP2D6-inhibitor:	0.007	CYP2D6-substrate:	0.985
CYP3A4-inhibitor:	0.001	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.998	CYP2C8-inhibitor:	1.0
HLM stability:	0.965 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

6.242

Half-life (T1/2):

0.183

ADMET: Toxicity

hERG Blockers:	0.156	hERG Blockers (10um):	0.555
Human Hepatotoxicity (H-HT):	0.137	Drug-induced Liver Injury (DILI):	0.014
AMES Toxicity:	0.247	Rat Oral Acute Toxicity:	0.061
Maximum Recommended Daily Dose:	0.072	Skin Sensitization:	0.998
Carcinogencity:	0.354	Eye Corrosion:	0.99
Eye Irritation:	0.997	Respiratory Toxicity:	0.567
Drug-induced Neurotoxicity:	0.028	Ototoxicity:	0.143
Hematotoxicity:	0.04	Drug-induced Nephrotoxicity:	0.136
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.028
A549 Cytotoxicity:	0.031	Hek293 Cytotoxicity:	0.028
BCF:	1.66 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	4.685 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.954 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.262 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO3375	Cystoseira barbata	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10508	Gossypium sturtianum	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO1144	Peucedanum alsaticum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8359	Phascolosoma vulgare	Species	Phascolosomatidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7791	Rhododendron makinoi	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10508	Gossypium sturtianum	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1144	Peucedanum alsaticum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7791	Rhododendron makinoi	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8359	Phascolosoma vulgare	Species	Phascolosomatidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3375	Cystoseira barbata	Species	Sargassaceae	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

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

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 NPC542578 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	26096
0.1-0.2	22136
0.2-0.3	1336
0.3-0.4	197
0.4-0.5	57
0.5-0.6	16
0.6-0.7	11
0.7-0.8	1
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC10316
1.0	High Similarity	NPC200845
0.871	High Similarity	NPC28779
0.7742	Intermediate Similarity	NPC128061
0.75	Intermediate Similarity	NPC139545
0.7297	Intermediate Similarity	NPC271921
0.675	Remote Similarity	NPC473772
0.6579	Remote Similarity	NPC475443
0.6579	Remote Similarity	NPC473829
0.6471	Remote Similarity	NPC39633
0.641	Remote Similarity	NPC330426
0.641	Remote Similarity	NPC127091
0.641	Remote Similarity	NPC22101
0.625	Remote Similarity	NPC54925
0.6207	Remote Similarity	NPC53541
0.6111	Remote Similarity	NPC223677
0.6	Remote Similarity	NPC71761
0.5806	Remote Similarity	NPC250028
0.5806	Remote Similarity	NPC236579
0.5806	Remote Similarity	NPC80234
0.5806	Remote Similarity	NPC203531
0.5806	Remote Similarity	NPC256163
0.5806	Remote Similarity	NPC40597
0.5789	Remote Similarity	NPC277597
0.575	Remote Similarity	NPC143857
0.575	Remote Similarity	NPC321919
0.575	Remote Similarity	NPC229252
0.5682	Remote Similarity	NPC473559
0.5682	Remote Similarity	NPC324981
0.5641	Remote Similarity	NPC104537
0.5588	Remote Similarity	NPC309606
0.5278	Remote Similarity	NPC207815
0.5135	Remote Similarity	NPC163345

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC542578 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6988
0.1-0.2	2026
0.2-0.3	111
0.3-0.4	20
0.4-0.5	2
0.5-0.6	0
0.6-0.7	0
0.7-0.8	1
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8667	High Similarity	NPD5343	Phase 4
0.8125	Intermediate Similarity	NPD6096	Phase 4
0.7419	Intermediate Similarity	NPD6097	Approved

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