Natural Product: NPC490195

Natural Product IDNPC490195
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Ethyl (Z,Z)-9,12-octadecadienoate
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
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

Standard InCHIKey FMMOOAYVCKXGMF-UONSLQGUSA-N
Standard InCHI InChI=1S/C20H36O2/c1-3-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20(21)22-4-2/h8-9,11-12H,3-7,10,13-19H2,1-2H3/b9-8-,12-11+
SMILES CCCCCC=C/CC=CCCCCCCCC(=O)OCC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   308.27 Volume:   364.147
?
Van der Waals volume.
Dense:   0.847 LogP:   7.152
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.187
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -6.715
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The logarithm of aqueous solubility value.
Rotatable Bonds:   16.0 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:   0.2 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.305 Fsp3:   0.75
MCE-18:   0.0
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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:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.257 Fluc inhibitor:   0.1
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.009
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.996 Promiscuous compounds:   0.365

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.012 MDCK Permeability:   -4.658
Pgp-inhibitor:   0.747 Pgp-substrate:   0.001
PAMPA:   0.001
?
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):   0.001
20% Bioavailability (F20%):   0.385 30% Bioavailability (F30%):   0.585
50% Bioavailability (F50%):   0.977

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.999
Plasma Protein Binding (PPB):   98.484% Volume Distribution (VD):   -0.459
Fu: 0.852%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.023
OATP1B3 inhibitor:   0.963 BCRP inhibitor:   0.131
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.002 CYP2C19-substrate:   0.999
CYP2C9-inhibitor:   0.99 CYP2C9-substrate:   0.016
CYP2D6-inhibitor:   0.664 CYP2D6-substrate:   0.999
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.995 CYP2C8-inhibitor:   1.0
HLM stability:   0.971
?
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):  6.181 Half-life (T1/2):  0.225

ADMET: Toxicity

hERG Blockers:  0.249 hERG Blockers (10um):  0.732
Human Hepatotoxicity (H-HT):  0.392 Drug-induced Liver Injury (DILI):  0.014
AMES Toxicity:  0.031 Rat Oral Acute Toxicity:  0.02
Maximum Recommended Daily Dose:  0.083 Skin Sensitization:  0.999
Carcinogencity:  0.085 Eye Corrosion:  0.86
Eye Irritation:  0.993 Respiratory Toxicity:  0.764
Drug-induced Neurotoxicity:  0.02 Ototoxicity:  0.167
Hematotoxicity:  0.029 Drug-induced Nephrotoxicity:  0.193
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.052
A549 Cytotoxicity:  0.18 Hek293 Cytotoxicity:  0.125
BCF:   1.432
?
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:   4.788
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.108
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.182
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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
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25340465]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. leaf n.a. PMID[25340465]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25577087]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[30827604]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[37331322]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[38719900]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2345 Coriandrum sativum Species Apiaceae 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
NPO2345 Coriandrum sativum Raw Fruit 8.95 1.3 16.6 mg/100g Database [DUKE]

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
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 NPC490195 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC28779
0.8966 High Similarity NPC128061
0.871 High Similarity NPC10316
0.871 High Similarity NPC200845
0.75 Intermediate Similarity NPC475443
0.75 Intermediate Similarity NPC473829
0.75 Intermediate Similarity NPC39633
0.7297 Intermediate Similarity NPC330426
0.7297 Intermediate Similarity NPC127091
0.7297 Intermediate Similarity NPC22101
0.7105 Intermediate Similarity NPC54925
0.7059 Intermediate Similarity NPC223677
0.6897 Remote Similarity NPC250028
0.6897 Remote Similarity NPC236579
0.6897 Remote Similarity NPC80234
0.6897 Remote Similarity NPC203531
0.6897 Remote Similarity NPC256163
0.6897 Remote Similarity NPC40597
0.6667 Remote Similarity NPC277597
0.6579 Remote Similarity NPC143857
0.6579 Remote Similarity NPC321919
0.6579 Remote Similarity NPC229252
0.6562 Remote Similarity NPC309606
0.6486 Remote Similarity NPC104537
0.6471 Remote Similarity NPC139545
0.6429 Remote Similarity NPC473559
0.6429 Remote Similarity NPC324981
0.641 Remote Similarity NPC271921
0.6207 Remote Similarity NPC53541
0.6 Remote Similarity NPC71761
0.5952 Remote Similarity NPC473772
0.5714 Remote Similarity NPC48218
0.5714 Remote Similarity NPC141481
0.5714 Remote Similarity NPC464342
0.5714 Remote Similarity NPC228473
0.5588 Remote Similarity NPC310746
0.55 Remote Similarity NPC81896
0.5385 Remote Similarity NPC148192
0.5366 Remote Similarity NPC476654
0.5366 Remote Similarity NPC476655
0.5366 Remote Similarity NPC476656
0.5294 Remote Similarity NPC600941
0.5294 Remote Similarity NPC603612
0.5192 Remote Similarity NPC470237
0.5143 Remote Similarity NPC149299
0.5135 Remote Similarity NPC163345
0.5094 Remote Similarity NPC489083

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC490195 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.75 Intermediate Similarity NPD5343 Phase 4
0.7059 Intermediate Similarity NPD6096 Phase 4
0.6364 Remote Similarity NPD6097 Approved

Bioactivity similarity

  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