Natural Product: NPC167186

Natural Product IDNPC167186
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 QWCNQXNAFCBLLV-OQDIJTRPSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 92043364
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols
          • [CHEMONTID:0002951] Long-chain fatty alcohols

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 QWCNQXNAFCBLLV-OQDIJTRPSA-N
Standard InCHI InChI=1S/C17H24O2/c1-3-5-6-7-8-9-10-14-17(19)15-12-11-13-16(18)4-2/h4,10,14,16-19H,2-3,5-9H2,1H3/b14-10-/t16-,17+/m0/s1
SMILES CCCCCCC/C=C[C@H](C#CC#C[C@H](C=C)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   260.18 Volume:   304.35
?
Van der Waals volume.
Dense:   0.855 LogP:   4.013
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.182
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.622
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   4.0
TPSA:   40.46
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   2.0 Rings:   0.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.4 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.118 Fsp3:   0.529
MCE-18:   2.0
?
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:   0.145 Fluc inhibitor:   0.001
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.017
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.774 Promiscuous compounds:   0.11

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.947 MDCK Permeability:   -4.665
Pgp-inhibitor:   0.006 Pgp-substrate:   0.0
PAMPA:   0.984
?
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):   0.0
20% Bioavailability (F20%):   0.0 30% Bioavailability (F30%):   0.002
50% Bioavailability (F50%):   0.978

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.0
Plasma Protein Binding (PPB):   97.709% Volume Distribution (VD):   -0.067
Fu: 1.762%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.0
OATP1B3 inhibitor:   0.004 BCRP inhibitor:   1.0
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.109 CYP2C19-substrate:   0.353
CYP2C9-inhibitor:   0.962 CYP2C9-substrate:   0.092
CYP2D6-inhibitor:   0.018 CYP2D6-substrate:   0.913
CYP3A4-inhibitor:   0.15 CYP3A4-substrate:   0.999
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.999
HLM stability:   0.321
?
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):  4.041 Half-life (T1/2):  1.444

ADMET: Toxicity

hERG Blockers:  0.06 hERG Blockers (10um):  0.76
Human Hepatotoxicity (H-HT):  0.229 Drug-induced Liver Injury (DILI):  0.296
AMES Toxicity:  0.319 Rat Oral Acute Toxicity:  0.647
Maximum Recommended Daily Dose:  0.623 Skin Sensitization:  0.984
Carcinogencity:  0.324 Eye Corrosion:  0.999
Eye Irritation:  0.998 Respiratory Toxicity:  1.0
Drug-induced Neurotoxicity:  0.169 Ototoxicity:  0.298
Hematotoxicity:  0.009 Drug-induced Nephrotoxicity:  0.033
Genotoxicity:  0.001 RPMI-8226 Immunitoxicity:  0.101
A549 Cytotoxicity:  0.328 Hek293 Cytotoxicity:  0.61
BCF:   1.608
?
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:   4.755
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.285
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.646
?
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
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. tenerife n.a. PMID[10924166]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[16309323]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[22220686]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. PMID[24279991]
NPO13803 Neopetrosia exigua Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[24784222]
NPO16201 Pteris altissima Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18716 Parmelia caraccensis Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13803 Neopetrosia exigua Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17606 Millettia ichthyochtona Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17281 Echinaster echinophorus Species Echinasteridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18250 Conus tessulatus Species Conidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19061 Ceratozamia kuesteriana Species Zamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17281 Echinaster echinophorus Species Echinasteridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13803 Neopetrosia exigua Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19061 Ceratozamia kuesteriana Species Zamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18716 Parmelia caraccensis Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18850 Aplysia dactylomela Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18250 Conus tessulatus Species Conidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16201 Pteris altissima Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17606 Millettia ichthyochtona Species Fabaceae 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
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 NPC167186 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 NPC91226
1.0 High Similarity NPC243546
1.0 High Similarity NPC31194
1.0 High Similarity NPC248884
0.8333 Intermediate Similarity NPC124183
0.8333 Intermediate Similarity NPC482802
0.7812 Intermediate Similarity NPC72699
0.7419 Intermediate Similarity NPC243813
0.7143 Intermediate Similarity NPC484320
0.7059 Intermediate Similarity NPC153538
0.7059 Intermediate Similarity NPC93639
0.6857 Remote Similarity NPC55063
0.6857 Remote Similarity NPC19834
0.6857 Remote Similarity NPC166942
0.6765 Remote Similarity NPC484322
0.6757 Remote Similarity NPC85079
0.6757 Remote Similarity NPC151782
0.6667 Remote Similarity NPC66460
0.6667 Remote Similarity NPC325929
0.6667 Remote Similarity NPC482801
0.6667 Remote Similarity NPC271282
0.6486 Remote Similarity NPC142092
0.6452 Remote Similarity NPC249670
0.625 Remote Similarity NPC474642
0.625 Remote Similarity NPC473913
0.6216 Remote Similarity NPC168510
0.5952 Remote Similarity NPC193975
0.5897 Remote Similarity NPC35141
0.5789 Remote Similarity NPC49059
0.5789 Remote Similarity NPC481849
0.5789 Remote Similarity NPC201681
0.5676 Remote Similarity NPC321763
0.5676 Remote Similarity NPC101616
0.5581 Remote Similarity NPC212730
0.5484 Remote Similarity NPC125122
0.5484 Remote Similarity NPC471276
0.5484 Remote Similarity NPC471280
0.5484 Remote Similarity NPC471281
0.5405 Remote Similarity NPC473865
0.5405 Remote Similarity NPC481854
0.5349 Remote Similarity NPC29697
0.5333 Remote Similarity NPC265551
0.5312 Remote Similarity NPC170776
0.5312 Remote Similarity NPC9273
0.5312 Remote Similarity NPC165447
0.5312 Remote Similarity NPC471959
0.5312 Remote Similarity NPC199286
0.5312 Remote Similarity NPC489046
0.5312 Remote Similarity NPC76198
0.5312 Remote Similarity NPC610719
0.525 Remote Similarity NPC48821
0.525 Remote Similarity NPC13418
0.5152 Remote Similarity NPC607242

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC167186 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
NPD

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