Natural Product: NPC539580

Natural Product IDNPC539580
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 3-methylbut-3-en-1-yl decanoate
IUPAC Name 3-methylbut-3-enyl decanoate
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 WATWBNKYNVTCSA-UHFFFAOYSA-N
Standard InCHI InChI=1S/C15H28O2/c1-4-5-6-7-8-9-10-11-15(16)17-13-12-14(2)3/h2,4-13H2,1,3H3
SMILES C=C(C)CCOC(=O)CCCCCCCCC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   240.21 Volume:   280.304
?
Van der Waals volume.
Dense:   0.857 LogP:   5.15
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.677
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.794
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The logarithm of aqueous solubility value.
Rotatable Bonds:   12.0 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:   0.299 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.091 Fsp3:   0.8
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:   Rejected BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.013 Fluc inhibitor:   0.036
?
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:   0.008
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.998 Promiscuous compounds:   0.13

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.011 MDCK Permeability:   -4.726
Pgp-inhibitor:   0.007 Pgp-substrate:   0.005
PAMPA:   0.01
?
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):   0.035
20% Bioavailability (F20%):   0.382 30% Bioavailability (F30%):   0.528
50% Bioavailability (F50%):   0.79

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.624 MRP1:   0.912
Plasma Protein Binding (PPB):   98.186% Volume Distribution (VD):   0.326
Fu: 2.013%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.605
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.383
BSEP inhibitor:   0.623

ADMET: Metabolism

CYP1A2-inhibitor:   0.002 CYP1A2-substrate:   0.999
CYP2C19-inhibitor:   0.026 CYP2C19-substrate:   0.174
CYP2C9-inhibitor:   0.501 CYP2C9-substrate:   0.673
CYP2D6-inhibitor:   0.079 CYP2D6-substrate:   0.468
CYP3A4-inhibitor:   0.008 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.245 CYP2C8-inhibitor:   0.995
HLM stability:   0.293
?
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):  6.075 Half-life (T1/2):  0.304

ADMET: Toxicity

hERG Blockers:  0.126 hERG Blockers (10um):  0.609
Human Hepatotoxicity (H-HT):  0.32 Drug-induced Liver Injury (DILI):  0.174
AMES Toxicity:  0.128 Rat Oral Acute Toxicity:  0.159
Maximum Recommended Daily Dose:  0.178 Skin Sensitization:  0.95
Carcinogencity:  0.618 Eye Corrosion:  0.993
Eye Irritation:  0.997 Respiratory Toxicity:  0.755
Drug-induced Neurotoxicity:  0.246 Ototoxicity:  0.174
Hematotoxicity:  0.254 Drug-induced Nephrotoxicity:  0.188
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.038
A549 Cytotoxicity:  0.05 Hek293 Cytotoxicity:  0.048
BCF:   1.316
?
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:   4.031
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.575
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.745
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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
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. leaf n.a. PMID[11348221]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[15844957]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota fruits n.a. n.a. PMID[16378361]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota fruits Tahiti n.a. PMID[17378609]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[17480098]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota roots n.a. n.a. PMID[18076142]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[24224843]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[27196335]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[32083868]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[36014413]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4323 Morinda citrifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4323 Morinda citrifolia Species Rubiaceae 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 NPC539580 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
0.7407 Intermediate Similarity NPC603612
0.7143 Intermediate Similarity NPC149299
0.6923 Remote Similarity NPC250028
0.6923 Remote Similarity NPC236579
0.6923 Remote Similarity NPC80234
0.6923 Remote Similarity NPC203531
0.6923 Remote Similarity NPC256163
0.6923 Remote Similarity NPC40597
0.6786 Remote Similarity NPC80396
0.6786 Remote Similarity NPC154642
0.6552 Remote Similarity NPC310746
0.6207 Remote Similarity NPC80641
0.6207 Remote Similarity NPC600941
0.6154 Remote Similarity NPC53541
0.6154 Remote Similarity NPC201622
0.6154 Remote Similarity NPC305660
0.6154 Remote Similarity NPC161097
0.6154 Remote Similarity NPC28598
0.6154 Remote Similarity NPC22903
0.6154 Remote Similarity NPC54980
0.6071 Remote Similarity NPC223249
0.6071 Remote Similarity NPC476550
0.6061 Remote Similarity NPC223677
0.5938 Remote Similarity NPC163345
0.5862 Remote Similarity NPC154396
0.5862 Remote Similarity NPC286695
0.5806 Remote Similarity NPC26253
0.5625 Remote Similarity NPC488257
0.5625 Remote Similarity NPC469937
0.5625 Remote Similarity NPC94699
0.5625 Remote Similarity NPC128061
0.5625 Remote Similarity NPC320588
0.5625 Remote Similarity NPC53463
0.5556 Remote Similarity NPC12156
0.5556 Remote Similarity NPC326758
0.5517 Remote Similarity NPC12904
0.5455 Remote Similarity NPC55678
0.5172 Remote Similarity NPC81263
0.5172 Remote Similarity NPC47363
0.5172 Remote Similarity NPC287231
0.5172 Remote Similarity NPC317128
0.5172 Remote Similarity NPC178643
0.5143 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 NPC539580 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
0.5455 Remote Similarity NPD6125 Phase 4
0.5357 Remote Similarity NPD900 Pre-clinical
0.5172 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