Natural Product: NPC204504

Natural Product IDNPC204504
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 BYCHQEILESTMQU-XFXZXTDPSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5365982
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001722] Fatty alcohol esters

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 BYCHQEILESTMQU-XFXZXTDPSA-N
Standard InCHI InChI=1S/C13H22O2/c1-5-13(14)15-10-9-12(4)8-6-7-11(2)3/h7,9H,5-6,8,10H2,1-4H3/b12-9-
SMILES CCC(=O)OC/C=C(/C)CCC=C(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   210.16 Volume:   243.075
?
Van der Waals volume.
Dense:   0.865 LogP:   4.492
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.318
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.035
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   3.0
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:   0.494 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.594 Fsp3:   0.615
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:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.035 Fluc inhibitor:   0.003
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.017
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.999 Promiscuous compounds:   0.084

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.582 MDCK Permeability:   -4.693
Pgp-inhibitor:   0.904 Pgp-substrate:   0.354
PAMPA:   0.018
?
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):   0.019
20% Bioavailability (F20%):   0.55 30% Bioavailability (F30%):   0.52
50% Bioavailability (F50%):   0.933

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.858 MRP1:   0.992
Plasma Protein Binding (PPB):   83.044% Volume Distribution (VD):   -0.519
Fu: 16.645%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.31
OATP1B3 inhibitor:   0.19 BCRP inhibitor:   0.261
BSEP inhibitor:   0.996

ADMET: Metabolism

CYP1A2-inhibitor:   0.089 CYP1A2-substrate:   0.067
CYP2C19-inhibitor:   0.708 CYP2C19-substrate:   0.005
CYP2C9-inhibitor:   0.31 CYP2C9-substrate:   0.012
CYP2D6-inhibitor:   0.186 CYP2D6-substrate:   0.06
CYP3A4-inhibitor:   0.049 CYP3A4-substrate:   0.245
CYP2B6-substrate:   0.015 CYP2C8-inhibitor:   0.61
HLM stability:   0.773
?
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):  8.853 Half-life (T1/2):  0.755

ADMET: Toxicity

hERG Blockers:  0.078 hERG Blockers (10um):  0.424
Human Hepatotoxicity (H-HT):  0.378 Drug-induced Liver Injury (DILI):  0.077
AMES Toxicity:  0.244 Rat Oral Acute Toxicity:  0.118
Maximum Recommended Daily Dose:  0.113 Skin Sensitization:  0.982
Carcinogencity:  0.502 Eye Corrosion:  0.942
Eye Irritation:  0.993 Respiratory Toxicity:  0.552
Drug-induced Neurotoxicity:  0.609 Ototoxicity:  0.22
Hematotoxicity:  0.327 Drug-induced Nephrotoxicity:  0.375
Genotoxicity:  0.006 RPMI-8226 Immunitoxicity:  0.035
A549 Cytotoxicity:  0.015 Hek293 Cytotoxicity:  0.023
BCF:   1.645
?
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:   4.023
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.525
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.893
?
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
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jep.2005.01.054]
NPO25148 Helichrysum italicum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[11678669]
NPO6414 Eupatorium cannabinum Species Asteraceae Eukaryota n.a. aerial part n.a. PMID[21391659]
NPO25148 Helichrysum italicum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[24094434]
NPO6414 Eupatorium cannabinum Species Asteraceae Eukaryota Aerial Parts n.a. n.a. PMID[30653318]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31181920]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31418264]
NPO542 Artemisia absinthium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[33588649]
NPO25148 Helichrysum italicum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[34762977]
NPO25148 Helichrysum italicum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[36235438]
NPO25148 Helichrysum italicum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[37513174]
NPO542 Artemisia absinthium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38538562]
NPO55098 Ambrosia acanthicarpa Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38543021]
NPO542 Artemisia absinthium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38606448]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38754641]
NPO542 Artemisia absinthium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[39598372]
NPO55098 Ambrosia acanthicarpa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6414 Eupatorium cannabinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO542 Artemisia absinthium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25148 Helichrysum italicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO542 Artemisia absinthium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6414 Eupatorium cannabinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25148 Helichrysum italicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO542 Artemisia absinthium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25148 Helichrysum italicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6414 Eupatorium cannabinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO542 Artemisia absinthium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6414 Eupatorium cannabinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO542 Artemisia absinthium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6414 Eupatorium cannabinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25148 Helichrysum italicum Species Asteraceae 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
NPO25148 Helichrysum italicum n.a. n.a. 1.74 ± 0.72 n.a. n.a. % PMID[36235438]
NPO25148 Helichrysum italicum n.a. n.a. 2.61 ± 0.57 n.a. n.a. % PMID[36235438]
NPO25148 Helichrysum italicum n.a. n.a. 1.1 ± 0.39 n.a. n.a. % PMID[36235438]
NPO25148 Helichrysum italicum Oil n.a. 0.00 n.a. n.a. % PMID[37513174]
NPO25148 Helichrysum italicum Oil n.a. 3.02 n.a. n.a. % PMID[37513174]
NPO25148 Helichrysum italicum Oil n.a. 2.10 n.a. n.a. % PMID[37513174]
NPO25148 Helichrysum italicum Oil n.a. 3.03 n.a. n.a. % PMID[37513174]
NPO25148 Helichrysum italicum Oil n.a. 1.76 n.a. n.a. % PMID[37513174]
NPO25148 Helichrysum italicum Oil n.a. 1.56 n.a. n.a. % PMID[37513174]
NPO25148 Helichrysum italicum Oil n.a. 3.25 n.a. n.a. % PMID[37513174]
NPO25148 Helichrysum italicum Oil n.a. 1.2 n.a. n.a. % PMID[34762977]
NPO25148 Helichrysum italicum Oil n.a. 5.6 n.a. n.a. % PMID[34762977]
NPO25148 Helichrysum italicum Oil n.a. 1.5 n.a. n.a. % PMID[34762977]
NPO25148 Helichrysum italicum Oil n.a. 2.5 n.a. n.a. % PMID[34762977]
NPO542 Artemisia absinthium Oil n.a. 0.2 n.a. n.a. % PMID[38538562]
NPO55098 Ambrosia acanthicarpa Oil n.a. 0.1 n.a. n.a. % PMID[38543021]

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
- Rattus norvegicus LD50 > 5000.0 mg/kg ToxVal
- Rattus norvegicus NOAEL = 345.0 mg/kg-day 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 NPC204504 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
0.8276 Intermediate Similarity NPC47946
0.8276 Intermediate Similarity NPC26600
0.8065 Intermediate Similarity NPC135698
0.7742 Intermediate Similarity NPC197467
0.7273 Intermediate Similarity NPC236338
0.5581 Remote Similarity NPC271641
0.5385 Remote Similarity NPC314590
0.5312 Remote Similarity NPC270706
0.5122 Remote Similarity NPC221379
0.5122 Remote Similarity NPC318549
0.5122 Remote Similarity NPC600969
0.5106 Remote Similarity NPC482044

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC204504 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
0.7576 Intermediate Similarity NPD6927 Phase 3

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