Natural Product: NPC71761

Natural Product IDNPC71761
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Omega-6-Hexadecenelactone
IUPAC Name (8Z)-1-oxacycloheptadec-8-en-2-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3727440
PubChem CID 5365703
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000147] Macrolides and analogues

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 NVIPUOMWGQAOIT-RQOWECAXSA-N
Standard InCHI InChI=1S/C16H28O2/c17-16-14-12-10-8-6-4-2-1-3-5-7-9-11-13-15-18-16/h2,4H,1,3,5-15H2/b4-2-
SMILES O=C1CCCCC/C=CCCCCCCCCO1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   252.21 Volume:   289.043
?
Van der Waals volume.
Dense:   0.873 LogP:   4.252
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.25
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.943
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   18.0
TPSA:   26.3
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   0.0 Rings:   1.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.458 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.744 Fsp3:   0.812
MCE-18:   7.586
?
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:   0.029 Fluc inhibitor:   0.227
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.004
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.012
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.997 Promiscuous compounds:   0.803

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.689 MDCK Permeability:   -4.759
Pgp-inhibitor:   0.874 Pgp-substrate:   0.0
PAMPA:   0.0
?
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%):   0.002 30% Bioavailability (F30%):   0.011
50% Bioavailability (F50%):   0.047

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.934 MRP1:   0.918
Plasma Protein Binding (PPB):   93.227% Volume Distribution (VD):   -0.157
Fu: 7.327%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.138
OATP1B3 inhibitor:   0.75 BCRP inhibitor:   0.083
BSEP inhibitor:   0.986

ADMET: Metabolism

CYP1A2-inhibitor:   0.509 CYP1A2-substrate:   0.033
CYP2C19-inhibitor:   0.03 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.036 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.018 CYP2D6-substrate:   0.012
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.953 CYP2C8-inhibitor:   0.947
HLM stability:   1.0
?
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):  5.992 Half-life (T1/2):  0.33

ADMET: Toxicity

hERG Blockers:  0.138 hERG Blockers (10um):  0.395
Human Hepatotoxicity (H-HT):  0.023 Drug-induced Liver Injury (DILI):  0.084
AMES Toxicity:  0.006 Rat Oral Acute Toxicity:  0.034
Maximum Recommended Daily Dose:  0.344 Skin Sensitization:  0.982
Carcinogencity:  0.042 Eye Corrosion:  1.0
Eye Irritation:  0.999 Respiratory Toxicity:  0.092
Drug-induced Neurotoxicity:  0.081 Ototoxicity:  0.073
Hematotoxicity:  0.023 Drug-induced Nephrotoxicity:  0.187
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.037
A549 Cytotoxicity:  0.077 Hek293 Cytotoxicity:  0.107
BCF:   1.031
?
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:   2.891
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.326
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.755
?
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
NPO242 Calycopteris floribunda Species Combretaceae Eukaryota n.a. n.a. n.a. PMID[21275386]
NPO43957 Alluaudia procera Species Didiereaceae Eukaryota n.a. n.a. n.a. PMID[31394879]
NPO242 Calycopteris floribunda Species Combretaceae Eukaryota n.a. n.a. n.a. PMID[35689756]
NPO14179 Campsis radicans Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[36201048]
NPO47617 Echinops polyceras Genus Asteraceae Eukaryota n.a. n.a. n.a. PMID[37241978]
NPO12563 Abelmoschus moschatus Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO242 Calycopteris floribunda Species Combretaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12563 Abelmoschus moschatus Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO242 Calycopteris floribunda Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12563 Abelmoschus moschatus Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12563 Abelmoschus moschatus Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14179 Campsis radicans Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12563 Abelmoschus moschatus Species Malvaceae 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
NPO14179 Campsis radicans Oil n.a. 5.44 n.a. n.a. % PMID[36201048]
NPO242 Calycopteris floribunda Acetone extract Flowers 10.78 n.a. n.a. % PMID[35689756]
NPO242 Calycopteris floribunda Ethanol extract Flowers 1.68 n.a. n.a. % PMID[35689756]
NPO43957 Alluaudia procera Oil n.a. 18.1 n.a. n.a. % PMID[31394879]
NPO47617 Echinops polyceras Hydro distillation Inflorescences 0.21 n.a. n.a. % PMID[37241978]
NPO47617 Echinops polyceras Hydro distillation Inflorescences 0.18 n.a. n.a. % PMID[37241978]

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
NPT603 Individual protein Olfactory receptor 5K1 Homo sapiens Inhibition >= 50.0 % Patent: WO2013171535 A3

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
- Rattus norvegicus LD50 = 339.0 mg/kg ToxVal
- Oryctolagus cuniculus LD50 > 5000.0 mg/kg ToxVal

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 NPC71761 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
0.8065 Intermediate Similarity NPC223677
0.7778 Intermediate Similarity NPC223249
0.7 Intermediate Similarity NPC149299
0.6667 Remote Similarity NPC80396
0.6562 Remote Similarity NPC128061
0.6562 Remote Similarity NPC207815
0.6129 Remote Similarity NPC154642
0.6129 Remote Similarity NPC80641
0.6129 Remote Similarity NPC603612
0.6 Remote Similarity NPC10316
0.6 Remote Similarity NPC200845
0.6 Remote Similarity NPC28779
0.5806 Remote Similarity NPC154396
0.5806 Remote Similarity NPC286695
0.5676 Remote Similarity NPC277597
0.5556 Remote Similarity NPC99700
0.5526 Remote Similarity NPC104537
0.5484 Remote Similarity NPC12904
0.5484 Remote Similarity NPC476550
0.5455 Remote Similarity NPC309606
0.5429 Remote Similarity NPC163345
0.525 Remote Similarity NPC475443
0.525 Remote Similarity NPC473829
0.5122 Remote Similarity NPC330426
0.5122 Remote Similarity NPC271921
0.5122 Remote Similarity NPC127091
0.5122 Remote Similarity NPC22101

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC71761 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