Natural Product: NPC103286

Natural Product IDNPC103286
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 6-Heptadecynoic Acid
IUPAC Name heptadec-6-ynoic acid
Synonyms 6-Heptadecynoic Acid
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1275976
PubChem CID 10264944
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 HNIQKLAUWGLVIK-UHFFFAOYSA-N
Standard InCHI InChI=1S/C17H30O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17(18)19/h2-10,13-16H2,1H3,(H,18,19)
SMILES CCCCCCCCCCC#CCCCCC(=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   266.22 Volume:   312.259
?
Van der Waals volume.
Dense:   0.853 LogP:   5.667
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.453
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.835
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   12.0 Rigid Bonds:   2.0
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:   0.391 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.206 Fsp3:   0.824
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:   0.009 Fluc inhibitor:   0.012
?
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:   0.991 Promiscuous compounds:   0.219

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.11 MDCK Permeability:   -4.768
Pgp-inhibitor:   0.0 Pgp-substrate:   0.008
PAMPA:   0.874
?
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):   0.606
20% Bioavailability (F20%):   0.087 30% Bioavailability (F30%):   0.109
50% Bioavailability (F50%):   0.068

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.048 MRP1:   0.93
Plasma Protein Binding (PPB):   97.755% Volume Distribution (VD):   0.645
Fu: 0.789%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.282
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.216
BSEP inhibitor:   0.664

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.027 CYP2C19-substrate:   1.0
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.499 CYP2D6-substrate:   0.009
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.996
CYP2B6-substrate:   1.0 CYP2C8-inhibitor:   1.0
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):  5.487 Half-life (T1/2):  0.585

ADMET: Toxicity

hERG Blockers:  0.063 hERG Blockers (10um):  0.183
Human Hepatotoxicity (H-HT):  0.409 Drug-induced Liver Injury (DILI):  0.144
AMES Toxicity:  0.244 Rat Oral Acute Toxicity:  0.288
Maximum Recommended Daily Dose:  0.58 Skin Sensitization:  0.999
Carcinogencity:  0.301 Eye Corrosion:  0.998
Eye Irritation:  0.998 Respiratory Toxicity:  0.986
Drug-induced Neurotoxicity:  0.04 Ototoxicity:  0.306
Hematotoxicity:  0.152 Drug-induced Nephrotoxicity:  0.516
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.03
A549 Cytotoxicity:  0.009 Hek293 Cytotoxicity:  0.219
BCF:   0.957
?
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:   4.095
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.561
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.28
?
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
NPO7415 Sommera sabiceoides Species Rubiaceae 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
NPT554 Organism Candida glabrata Candida glabrata IC50 > 187700.0 nM PMID[18458131]
NPT21 Organism Aspergillus niger Aspergillus niger IC50 > 187700.0 nM PMID[18458131]
NPT20 Organism Candida albicans Candida albicans IC50 > 187700.0 nM PMID[18458131]
NPT20 Organism Candida albicans Candida albicans IC50 = 150000.0 nM PMID[18458131]
NPT20 Organism Candida albicans Candida albicans IC50 = 187700.0 nM PMID[18458131]
NPT20 Organism Candida albicans Candida albicans IC50 = 95400.0 nM PMID[18458131]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes IC50 = 3000.0 nM PMID[18458131]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes IC50 = 3700.0 nM PMID[18458131]
NPT329 Organism Trichophyton rubrum Trichophyton rubrum IC50 = 4100.0 nM PMID[18458131]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes MIC = 5900.0 nM PMID[18458131]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes MFC = 5.9 uM PMID[18458131]
NPT329 Organism Trichophyton rubrum Trichophyton rubrum IC50 = 6500.0 nM PMID[18458131]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes MIC = 7300.0 nM PMID[18458131]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes MFC = 11.7 uM PMID[18458131]
NPT329 Organism Trichophyton rubrum Trichophyton rubrum MIC = 17600.0 nM PMID[18458131]
NPT20 Organism Candida albicans Candida albicans IC50 = 18800.0 nM PMID[18458131]
NPT329 Organism Trichophyton rubrum Trichophyton rubrum MFC = 23.5 uM PMID[18458131]
NPT329 Organism Trichophyton rubrum Trichophyton rubrum MIC = 29300.0 nM PMID[18458131]
NPT20 Organism Candida albicans Candida albicans IC50 = 66700.0 nM PMID[18458131]
NPT20 Organism Candida albicans Candida albicans MIC = 70400.0 nM PMID[18458131]
NPT20 Organism Candida albicans Candida albicans IC50 = 82200.0 nM PMID[18458131]
NPT85 Organism Filobasidiella neoformans Cryptococcus neoformans IC50 = 1200.0 nM PMID[18458131]
NPT187 Organism Issatchenkia orientalis Pichia kudriavzevii IC50 = 1900.0 nM PMID[18458131]
NPT187 Organism Issatchenkia orientalis Pichia kudriavzevii MIC = 4400.0 nM PMID[18458131]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus IC50 = 36600.0 nM PMID[18458131]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus MIC = 140800.0 nM PMID[18458131]
NPT85 Organism Filobasidiella neoformans Cryptococcus neoformans MIC = 187700.0 nM PMID[18458131]
NPT85 Organism Filobasidiella neoformans Cryptococcus neoformans IC50 > 187700.0 nM PMID[18458131]
NPT186 Organism Candida tropicalis Candida tropicalis IC50 = 49100.0 nM PMID[18458131]

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 NPC103286 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 NPC129972
1.0 High Similarity NPC301528
1.0 High Similarity NPC71317
1.0 High Similarity NPC163746
0.9259 High Similarity NPC8219
0.7419 Intermediate Similarity NPC158179
0.7097 Intermediate Similarity NPC73245
0.7037 Intermediate Similarity NPC171736
0.7037 Intermediate Similarity NPC301585
0.7037 Intermediate Similarity NPC261080
0.7037 Intermediate Similarity NPC132565
0.7037 Intermediate Similarity NPC209970
0.7037 Intermediate Similarity NPC216630
0.7037 Intermediate Similarity NPC201844
0.7037 Intermediate Similarity NPC301696
0.7037 Intermediate Similarity NPC196924
0.7037 Intermediate Similarity NPC307783
0.7037 Intermediate Similarity NPC154186
0.7037 Intermediate Similarity NPC149184
0.7037 Intermediate Similarity NPC279026
0.7037 Intermediate Similarity NPC113928
0.7037 Intermediate Similarity NPC14227
0.6786 Remote Similarity NPC604140
0.6667 Remote Similarity NPC155263
0.6316 Remote Similarity NPC179764
0.6296 Remote Similarity NPC175342
0.5946 Remote Similarity NPC284212
0.5926 Remote Similarity NPC214610
0.5926 Remote Similarity NPC118968
0.5926 Remote Similarity NPC183424
0.5926 Remote Similarity NPC294085
0.5789 Remote Similarity NPC304162
0.5769 Remote Similarity NPC174368
0.5758 Remote Similarity NPC424
0.5758 Remote Similarity NPC36061
0.5758 Remote Similarity NPC69510
0.5758 Remote Similarity NPC77272
0.5758 Remote Similarity NPC290563
0.5758 Remote Similarity NPC139029
0.5758 Remote Similarity NPC281972
0.5758 Remote Similarity NPC92114
0.5758 Remote Similarity NPC261831
0.5758 Remote Similarity NPC87564
0.575 Remote Similarity NPC187777
0.575 Remote Similarity NPC473863
0.5676 Remote Similarity NPC18357
0.5641 Remote Similarity NPC28205
0.5588 Remote Similarity NPC18712
0.5588 Remote Similarity NPC74845
0.5588 Remote Similarity NPC95145
0.5588 Remote Similarity NPC325642
0.5588 Remote Similarity NPC65174
0.5556 Remote Similarity NPC134782
0.5556 Remote Similarity NPC268826
0.55 Remote Similarity NPC485704
0.55 Remote Similarity NPC274290
0.5455 Remote Similarity NPC281245
0.5429 Remote Similarity NPC87394
0.5429 Remote Similarity NPC324004
0.5429 Remote Similarity NPC328497
0.5429 Remote Similarity NPC602547
0.5312 Remote Similarity NPC55023
0.5312 Remote Similarity NPC21844
0.5278 Remote Similarity NPC154245
0.5278 Remote Similarity NPC85813
0.5278 Remote Similarity NPC223697
0.5278 Remote Similarity NPC6095
0.5122 Remote Similarity NPC100096
0.5116 Remote Similarity NPC226592

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC103286 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
0.7037 Intermediate Similarity NPD2270 Pre-clinical
0.7037 Intermediate Similarity NPD633 Phase 3
0.7037 Intermediate Similarity NPD9448 Phase 2
0.5926 Remote Similarity NPD9655 Phase 4
0.5758 Remote Similarity NPD3195 Phase 2
0.5758 Remote Similarity NPD3196 Approved
0.5429 Remote Similarity NPD3199 Clinical (unspecified phase)
0.5278 Remote Similarity NPD4266 Phase 2

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