Natural Product: NPC519302

Natural Product IDNPC519302
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 3-methyl-3-hexen-1-yl butanoate
IUPAC Name 3-methylhex-3-enyl butanoate
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 SMJVHJPBTMEGCQ-UHFFFAOYSA-N
Standard InCHI InChI=1S/C11H20O2/c1-4-6-10(3)8-9-13-11(12)7-5-2/h6H,4-5,7-9H2,1-3H3
SMILES CCC=C(C)CCOC(=O)CCC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   184.15 Volume:   211.12
?
Van der Waals volume.
Dense:   0.872 LogP:   3.749
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.097
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.329
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The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   2.0
TPSA:   26.3
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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:   0.468 GASA:   0.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.445 Fsp3:   0.727
MCE-18:   0.0
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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:   Rejected
Golden Triangle Rule:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.019 Fluc inhibitor:   0.001
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.004
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   1.0 Promiscuous compounds:   0.084

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.552 MDCK Permeability:   -4.621
Pgp-inhibitor:   0.481 Pgp-substrate:   0.328
PAMPA:   0.108
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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):   0.097
20% Bioavailability (F20%):   0.39 30% Bioavailability (F30%):   0.446
50% Bioavailability (F50%):   0.953

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.783 MRP1:   0.93
Plasma Protein Binding (PPB):   87.332% Volume Distribution (VD):   -0.326
Fu: 13.069%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.556
OATP1B3 inhibitor:   0.877 BCRP inhibitor:   0.08
BSEP inhibitor:   0.99

ADMET: Metabolism

CYP1A2-inhibitor:   0.956 CYP1A2-substrate:   0.982
CYP2C19-inhibitor:   0.237 CYP2C19-substrate:   0.694
CYP2C9-inhibitor:   0.012 CYP2C9-substrate:   0.117
CYP2D6-inhibitor:   0.018 CYP2D6-substrate:   0.519
CYP3A4-inhibitor:   0.763 CYP3A4-substrate:   0.926
CYP2B6-substrate:   0.14 CYP2C8-inhibitor:   0.987
HLM stability:   0.998
?
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):  7.43 Half-life (T1/2):  0.313

ADMET: Toxicity

hERG Blockers:  0.068 hERG Blockers (10um):  0.437
Human Hepatotoxicity (H-HT):  0.321 Drug-induced Liver Injury (DILI):  0.199
AMES Toxicity:  0.183 Rat Oral Acute Toxicity:  0.125
Maximum Recommended Daily Dose:  0.186 Skin Sensitization:  0.787
Carcinogencity:  0.577 Eye Corrosion:  0.969
Eye Irritation:  0.99 Respiratory Toxicity:  0.45
Drug-induced Neurotoxicity:  0.404 Ototoxicity:  0.172
Hematotoxicity:  0.317 Drug-induced Nephrotoxicity:  0.294
Genotoxicity:  0.007 RPMI-8226 Immunitoxicity:  0.048
A549 Cytotoxicity:  0.025 Hek293 Cytotoxicity:  0.05
BCF:   0.75
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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:   3.119
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.394
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.016
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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
NPO20404 Eruca vesicaria Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[19489541]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota aerial parts and buds Cagliari, Sardinia 2012-FEB PMID[22769561]
NPO20404 Eruca vesicaria Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[31361076]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20404 Eruca vesicaria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20404 Eruca vesicaria Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1099 Capparis spinosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]

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
NPO20404 Eruca vesicaria Oil n.a. 0.7 n.a. n.a. % PMID[31361076]

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 NPC519302 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
0.5926 Remote Similarity NPC326758
0.5667 Remote Similarity NPC154396
0.5517 Remote Similarity NPC178643
0.5484 Remote Similarity NPC80641
0.5333 Remote Similarity NPC12904
0.5294 Remote Similarity NPC163345
0.5185 Remote Similarity NPC143211

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC519302 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
0.5172 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