Natural Product: NPC492653

Natural Product IDNPC492653
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 2-HEPTYL BUTYRATE
IUPAC Name 1-methylhexyl 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 GTKUPJHQSAPWLL-UHFFFAOYSA-N
Standard InCHI InChI=1S/C11H22O2/c1-4-6-7-9-10(3)13-11(12)8-5-2/h10H,4-9H2,1-3H3
SMILES CCCCCC(C)OC(=O)CCC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   186.16 Volume:   213.756
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Van der Waals volume.
Dense:   0.871 LogP:   3.954
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.236
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.526
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The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   1.0
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:   0.45 GASA:   0.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.423 Fsp3:   0.909
MCE-18:   2.0
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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:   0.013 Fluc inhibitor:   0.0
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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:   0.001
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.999 Promiscuous compounds:   0.009

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.857 MDCK Permeability:   -4.708
Pgp-inhibitor:   0.226 Pgp-substrate:   0.367
PAMPA:   0.051
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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):   0.145
20% Bioavailability (F20%):   0.258 30% Bioavailability (F30%):   0.589
50% Bioavailability (F50%):   0.939

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.843 MRP1:   0.918
Plasma Protein Binding (PPB):   94.077% Volume Distribution (VD):   0.169
Fu: 5.975%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.427
OATP1B3 inhibitor:   0.986 BCRP inhibitor:   0.675
BSEP inhibitor:   0.957

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.942
CYP2C19-inhibitor:   0.975 CYP2C19-substrate:   0.427
CYP2C9-inhibitor:   0.13 CYP2C9-substrate:   0.715
CYP2D6-inhibitor:   0.073 CYP2D6-substrate:   0.986
CYP3A4-inhibitor:   0.989 CYP3A4-substrate:   0.463
CYP2B6-substrate:   0.917 CYP2C8-inhibitor:   0.999
HLM stability:   0.95
?
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):  6.275 Half-life (T1/2):  0.38

ADMET: Toxicity

hERG Blockers:  0.253 hERG Blockers (10um):  0.671
Human Hepatotoxicity (H-HT):  0.363 Drug-induced Liver Injury (DILI):  0.227
AMES Toxicity:  0.114 Rat Oral Acute Toxicity:  0.195
Maximum Recommended Daily Dose:  0.191 Skin Sensitization:  0.802
Carcinogencity:  0.375 Eye Corrosion:  0.986
Eye Irritation:  0.994 Respiratory Toxicity:  0.605
Drug-induced Neurotoxicity:  0.21 Ototoxicity:  0.204
Hematotoxicity:  0.184 Drug-induced Nephrotoxicity:  0.466
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.064
A549 Cytotoxicity:  0.151 Hek293 Cytotoxicity:  0.08
BCF:   1.538
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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:   3.417
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.486
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.238
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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
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. n.a. PMID[21608987]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota 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 Fruit Juice n.a. n.a. Database[FooDB]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. Database[FooDB]
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]
NPO10856 Passiflora edulis Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
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 NPC492653 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
0.6667 Remote Similarity NPC105329
0.6667 Remote Similarity NPC321699
0.64 Remote Similarity NPC63182
0.64 Remote Similarity NPC145045
0.64 Remote Similarity NPC52700
0.6 Remote Similarity NPC273545
0.5926 Remote Similarity NPC603863
0.5833 Remote Similarity NPC176500
0.5769 Remote Similarity NPC47363
0.5769 Remote Similarity NPC287231
0.5769 Remote Similarity NPC326957
0.5417 Remote Similarity NPC94368
0.5161 Remote Similarity NPC609089

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC492653 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
0.5769 Remote Similarity NPD2699 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