Natural Product: NPC207292

Natural Product IDNPC207292
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (6Z,9Z,12Z,15Z)-Hexadecatetraenoic Acid
IUPAC Name (6Z,9Z,12Z)-hexadeca-6,9,12,15-tetraenoic acid
Synonyms (6Z,9Z,12Z,15Z)-Hexadecatetraenoic Acid
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL475064
PubChem CID 11957734
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0002949] Long-chain fatty acids

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 OKBAWLHHZWRDBE-YSTUJMKBSA-N
Standard InCHI InChI=1S/C16H24O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16(17)18/h2,4-5,7-8,10-11H,1,3,6,9,12-15H2,(H,17,18)/b5-4-,8-7-,11-10-
SMILES C=CC/C=CC/C=CC/C=CCCCCC(=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   248.18 Volume:   289.69
?
Van der Waals volume.
Dense:   0.857 LogP:   5.535
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.239
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.838
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   11.0 Rigid Bonds:   5.0
TPSA:   37.3
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   1.0 Rings:   0.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.426 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.869 Fsp3:   0.438
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:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.006 Fluc inhibitor:   0.305
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.006
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.015
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.999 Promiscuous compounds:   0.573

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.984 MDCK Permeability:   -4.748
Pgp-inhibitor:   0.015 Pgp-substrate:   0.0
PAMPA:   0.067
?
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%):   0.06 30% Bioavailability (F30%):   0.278
50% Bioavailability (F50%):   0.498

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.04 MRP1:   0.99
Plasma Protein Binding (PPB):   97.598% Volume Distribution (VD):   -0.404
Fu: 2.533%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.117
OATP1B3 inhibitor:   0.649 BCRP inhibitor:   0.14
BSEP inhibitor:   0.737

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.959 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   1.0 CYP2C8-inhibitor:   0.999
HLM stability:   0.0
?
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):  6.621 Half-life (T1/2):  0.239

ADMET: Toxicity

hERG Blockers:  0.097 hERG Blockers (10um):  0.317
Human Hepatotoxicity (H-HT):  0.005 Drug-induced Liver Injury (DILI):  0.0
AMES Toxicity:  0.573 Rat Oral Acute Toxicity:  0.06
Maximum Recommended Daily Dose:  0.001 Skin Sensitization:  1.0
Carcinogencity:  0.003 Eye Corrosion:  1.0
Eye Irritation:  1.0 Respiratory Toxicity:  0.981
Drug-induced Neurotoxicity:  0.038 Ototoxicity:  0.033
Hematotoxicity:  0.0 Drug-induced Nephrotoxicity:  0.05
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.011
A549 Cytotoxicity:  0.018 Hek293 Cytotoxicity:  0.004
BCF:   1.175
?
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:   3.792
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.124
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.947
?
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
NPO28813 Xylocarpus granatum Species Meliaceae Eukaryota n.a. rind n.a. DOI[10.1002/hlca.200800177]
NPO28813 Xylocarpus granatum Species Meliaceae Eukaryota seeds n.a. n.a. PMID[17323995]
NPO28813 Xylocarpus granatum Species Meliaceae Eukaryota n.a. bark n.a. PMID[17450509]
NPO28813 Xylocarpus granatum Species Meliaceae Eukaryota seed kernels n.a. n.a. PMID[19908853]
NPO28813 Xylocarpus granatum Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[20411928]
NPO28813 Xylocarpus granatum Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[31895570]
NPO7946 Navicula delognei Species Berkeleyaceae Eukaryota n.a. n.a. n.a. PMID[6512534]
NPO6111 Amaryllis minuta Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27982 Brevoortia tyrannus Species Clupeidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28872 Cacia confusa n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO28340 Coleus rehneltianus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4603 Eriostemon trachyphyllus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28093 Gelidium sesquipedale Species Gelidiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28602 Geniostoma antherotrichum Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25672 Hypnum plumaeforme Species Hypnaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28908 Pelagomonas calceolata Species n.a. Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28929 Penicillium jensenii Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28637 Phlomis amanica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28677 Pisonia umbellifera Species Nyctaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28307 Rumex abyssinicus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28486 Salvia viridis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28813 Xylocarpus granatum Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7946 Navicula delognei Species Berkeleyaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27982 Brevoortia tyrannus Species Clupeidae Eukaryota n.a. n.a. Database[FooDB]
NPO27982 Brevoortia tyrannus Species Clupeidae Eukaryota n.a. n.a. Database[FooDB]
NPO6111 Amaryllis minuta Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7946 Navicula delognei Species Berkeleyaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28677 Pisonia umbellifera Species Nyctaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28872 Cacia confusa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO7946 Navicula delognei Species Berkeleyaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28637 Phlomis amanica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28602 Geniostoma antherotrichum Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28908 Pelagomonas calceolata Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28340 Coleus rehneltianus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28813 Xylocarpus granatum Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28486 Salvia viridis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27982 Brevoortia tyrannus Species Clupeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25672 Hypnum plumaeforme Species Hypnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6111 Amaryllis minuta Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4603 Eriostemon trachyphyllus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28307 Rumex abyssinicus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28929 Penicillium jensenii Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28093 Gelidium sesquipedale Species Gelidiaceae 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
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium IZ > 4.0 mm PMID[6512534]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ > 2.0 mm PMID[6512534]
NPT17 Organism Staphylococcus epidermidis Staphylococcus epidermidis IZ > 2.0 mm PMID[6512534]

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 NPC207292 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
0.8 Intermediate Similarity NPC149821
0.7742 Intermediate Similarity NPC5413
0.7188 Intermediate Similarity NPC321062
0.7188 Intermediate Similarity NPC70387
0.697 Remote Similarity NPC52955
0.697 Remote Similarity NPC88966
0.697 Remote Similarity NPC25417
0.697 Remote Similarity NPC1813
0.697 Remote Similarity NPC154245
0.697 Remote Similarity NPC85813
0.697 Remote Similarity NPC223697
0.697 Remote Similarity NPC6095
0.6667 Remote Similarity NPC91495
0.6562 Remote Similarity NPC92114
0.6471 Remote Similarity NPC59051
0.625 Remote Similarity NPC117572
0.625 Remote Similarity NPC281245
0.6129 Remote Similarity NPC180534
0.6129 Remote Similarity NPC611531
0.6061 Remote Similarity NPC424
0.6061 Remote Similarity NPC36061
0.6061 Remote Similarity NPC69510
0.6061 Remote Similarity NPC77272
0.6061 Remote Similarity NPC290563
0.6061 Remote Similarity NPC139029
0.6061 Remote Similarity NPC281972
0.6061 Remote Similarity NPC261831
0.6061 Remote Similarity NPC87564
0.561 Remote Similarity NPC323597
0.561 Remote Similarity NPC211752
0.561 Remote Similarity NPC323498
0.5476 Remote Similarity NPC317583
0.5429 Remote Similarity NPC95145
0.5429 Remote Similarity NPC325642
0.5429 Remote Similarity NPC65174
0.5357 Remote Similarity NPC134782
0.5357 Remote Similarity NPC268826
0.5278 Remote Similarity NPC48162
0.5172 Remote Similarity NPC214610
0.5172 Remote Similarity NPC118968
0.5172 Remote Similarity NPC183424
0.5172 Remote Similarity NPC294085
0.5116 Remote Similarity NPC320305

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC207292 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
0.7742 Intermediate Similarity NPD3173 Phase 4
0.697 Remote Similarity NPD3172 Approved
0.697 Remote Similarity NPD4266 Phase 2
0.625 Remote Similarity NPD4222 Phase 3
0.6129 Remote Similarity NPD622 Pre-clinical
0.6061 Remote Similarity NPD3195 Phase 2
0.6061 Remote Similarity NPD3196 Approved
0.5854 Remote Similarity NPD39 Phase 4
0.5172 Remote Similarity NPD9655 Phase 4

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