Natural Product: NPC506569

Natural Product IDNPC506569
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 MFCD00036552
IUPAC Name hex-3-enyl hexanoate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 RGACQXBDYBCJCY-UHFFFAOYSA-N
Standard InCHI InChI=1S/C12H22O2/c1-3-5-7-9-11-14-12(13)10-8-6-4-2/h5,7H,3-4,6,8-11H2,1-2H3
SMILES CCC=CCCOC(=O)CCCCC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   198.16 Volume:   228.416
?
Van der Waals volume.
Dense:   0.868 LogP:   4.043
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.209
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.538
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   9.0 Rigid Bonds:   2.0
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:   0.339 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.188 Fsp3:   0.75
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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.014 Fluc inhibitor:   0.007
?
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:   0.007
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   1.0 Promiscuous compounds:   0.266

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.733 MDCK Permeability:   -4.656
Pgp-inhibitor:   0.417 Pgp-substrate:   0.178
PAMPA:   0.056
?
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):   0.036
20% Bioavailability (F20%):   0.366 30% Bioavailability (F30%):   0.374
50% Bioavailability (F50%):   0.604

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.837 MRP1:   0.825
Plasma Protein Binding (PPB):   95.874% Volume Distribution (VD):   -0.533
Fu: 4.774%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.048
OATP1B3 inhibitor:   0.382 BCRP inhibitor:   0.164
BSEP inhibitor:   0.994

ADMET: Metabolism

CYP1A2-inhibitor:   0.04 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.479 CYP2C19-substrate:   0.996
CYP2C9-inhibitor:   0.055 CYP2C9-substrate:   0.656
CYP2D6-inhibitor:   0.03 CYP2D6-substrate:   0.999
CYP3A4-inhibitor:   0.055 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.075 CYP2C8-inhibitor:   1.0
HLM stability:   0.997
?
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):  6.855 Half-life (T1/2):  0.243

ADMET: Toxicity

hERG Blockers:  0.136 hERG Blockers (10um):  0.558
Human Hepatotoxicity (H-HT):  0.295 Drug-induced Liver Injury (DILI):  0.173
AMES Toxicity:  0.262 Rat Oral Acute Toxicity:  0.166
Maximum Recommended Daily Dose:  0.18 Skin Sensitization:  0.77
Carcinogencity:  0.492 Eye Corrosion:  0.988
Eye Irritation:  0.994 Respiratory Toxicity:  0.607
Drug-induced Neurotoxicity:  0.262 Ototoxicity:  0.143
Hematotoxicity:  0.18 Drug-induced Nephrotoxicity:  0.279
Genotoxicity:  0.001 RPMI-8226 Immunitoxicity:  0.049
A549 Cytotoxicity:  0.052 Hek293 Cytotoxicity:  0.071
BCF:   1.168
?
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:   3.703
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.098
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.746
?
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
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. n.a. DOI[10.1007/BF00232372]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. Granola: the 1999 growing season DOI[10.1016/S0956-7135(03)00077-X]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. seeds n.a. n.a. PMID[12105963]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. n.a. PMID[21608987]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. n.a. PMID[2831703]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. Database[FooDB]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. Database[FooDB]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota Fruit Juice n.a. n.a. Database[FooDB]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. Database[FooDB]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. Database[Phenol-Explorer]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10856 Passiflora edulis Species Passifloraceae 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 NPC506569 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 NPC163345
0.6897 Remote Similarity NPC123357
0.6667 Remote Similarity NPC80396
0.6667 Remote Similarity NPC154642
0.6667 Remote Similarity NPC603612
0.6471 Remote Similarity NPC223677
0.6452 Remote Similarity NPC149299
0.6207 Remote Similarity NPC226511
0.6 Remote Similarity NPC476550
0.5806 Remote Similarity NPC154396
0.5806 Remote Similarity NPC286695
0.5758 Remote Similarity NPC15789
0.5667 Remote Similarity NPC250028
0.5667 Remote Similarity NPC236579
0.5667 Remote Similarity NPC80234
0.5667 Remote Similarity NPC203531
0.5667 Remote Similarity NPC256163
0.5667 Remote Similarity NPC40597
0.5625 Remote Similarity NPC187922
0.5625 Remote Similarity NPC80641
0.5625 Remote Similarity NPC600941
0.5588 Remote Similarity NPC128061
0.5484 Remote Similarity NPC223249
0.5484 Remote Similarity NPC12904
0.5455 Remote Similarity NPC310746
0.5429 Remote Similarity NPC71761
0.5135 Remote Similarity NPC10316
0.5135 Remote Similarity NPC200845
0.5135 Remote Similarity NPC28779

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC506569 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
0.5333 Remote Similarity NPD900 Pre-clinical

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