Natural Product: NPC210497

Natural Product IDNPC210497
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 5-{8(Z),11(Z)-Pentadecadienyl}Phenol
IUPAC Name 3-[(8Z,11Z)-pentadeca-8,11-dienyl]phenol
Synonyms 5-{8(Z),11(Z)-Pentadecadienyl}Phenol
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL470887
PubChem CID 11098630
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000134] Phenols
        • [CHEMONTID:0004647] 1-hydroxy-4-unsubstituted benzenoids

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 FAYVLNWNMNHXGA-UTOQUPLUSA-N
Standard InCHI InChI=1S/C21H32O/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-16-20-17-15-18-21(22)19-20/h4-5,7-8,15,17-19,22H,2-3,6,9-14,16H2,1H3/b5-4-,8-7-
SMILES CCC/C=CC/C=CCCCCCCCc1cccc(c1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   300.25 Volume:   358.824
?
Van der Waals volume.
Dense:   0.837 LogP:   7.85
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.568
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -7.193
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   12.0 Rigid Bonds:   8.0
TPSA:   20.23
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   1.0 Rings:   1.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.341 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.35 Fsp3:   0.524
MCE-18:   5.0
?
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:   0.674 Fluc inhibitor:   0.37
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.004
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.223
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.982 Promiscuous compounds:   0.158

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.037 MDCK Permeability:   -4.74
Pgp-inhibitor:   0.847 Pgp-substrate:   0.004
PAMPA:   0.001
?
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):   0.007
20% Bioavailability (F20%):   0.789 30% Bioavailability (F30%):   0.961
50% Bioavailability (F50%):   0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.031 MRP1:   0.947
Plasma Protein Binding (PPB):   98.962% Volume Distribution (VD):   0.493
Fu: 0.579%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.303
OATP1B3 inhibitor:   0.81 BCRP inhibitor:   0.782
BSEP inhibitor:   0.998

ADMET: Metabolism

CYP1A2-inhibitor:   0.003 CYP1A2-substrate:   0.998
CYP2C19-inhibitor:   0.041 CYP2C19-substrate:   0.434
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.182
CYP2D6-inhibitor:   0.992 CYP2D6-substrate:   0.995
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.912 CYP2C8-inhibitor:   1.0
HLM stability:   0.617
?
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):  5.877 Half-life (T1/2):  0.214

ADMET: Toxicity

hERG Blockers:  0.68 hERG Blockers (10um):  0.866
Human Hepatotoxicity (H-HT):  0.221 Drug-induced Liver Injury (DILI):  0.0
AMES Toxicity:  0.38 Rat Oral Acute Toxicity:  0.037
Maximum Recommended Daily Dose:  0.02 Skin Sensitization:  1.0
Carcinogencity:  0.008 Eye Corrosion:  1.0
Eye Irritation:  1.0 Respiratory Toxicity:  0.875
Drug-induced Neurotoxicity:  0.062 Ototoxicity:  0.085
Hematotoxicity:  0.001 Drug-induced Nephrotoxicity:  0.408
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.052
A549 Cytotoxicity:  0.927 Hek293 Cytotoxicity:  0.27
BCF:   1.894
?
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:   5.287
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.203
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.112
?
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
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota Fruits n.a. n.a. PMID[8021657]
NPO13016 Viscaria viscosa Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12510 Aronia arbutifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13070 Clibadium mexiae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1744 Discaria serratifolia Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11636 Ideopsis similis Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO998 Justicia hayatai Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3469 Pteris dactylina Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9180 Pyrostegia venusta Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3580 Rana amurensis Species Ranidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3469 Pteris dactylina Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3580 Rana amurensis Species Ranidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3580 Rana amurensis Species Ranidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13070 Clibadium mexiae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12510 Aronia arbutifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3469 Pteris dactylina Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11636 Ideopsis similis Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13016 Viscaria viscosa Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3580 Rana amurensis Species Ranidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO998 Justicia hayatai Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9180 Pyrostegia venusta Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1744 Discaria serratifolia Species Rhamnaceae 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
NPT89 Individual protein Seed lipoxygenase-1 Glycine max IC50 = 125000.0 nM DOI[10.1021/np50114a025]

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 NPC210497 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
0.8974 High Similarity NPC483454
0.8974 High Similarity NPC162314
0.875 High Similarity NPC94139
0.875 High Similarity NPC147284
0.8571 High Similarity NPC192
0.825 Intermediate Similarity NPC487734
0.7442 Intermediate Similarity NPC302219
0.725 Intermediate Similarity NPC3358
0.725 Intermediate Similarity NPC306884
0.725 Intermediate Similarity NPC603092
0.7045 Intermediate Similarity NPC71002
0.7045 Intermediate Similarity NPC249828
0.6818 Remote Similarity NPC487735
0.6667 Remote Similarity NPC242342
0.6667 Remote Similarity NPC85479
0.6596 Remote Similarity NPC48730
0.6522 Remote Similarity NPC158253
0.6512 Remote Similarity NPC53051
0.6512 Remote Similarity NPC24404
0.6512 Remote Similarity NPC313030
0.6429 Remote Similarity NPC76938
0.6429 Remote Similarity NPC32714
0.6364 Remote Similarity NPC146798
0.6364 Remote Similarity NPC222522
0.6364 Remote Similarity NPC106396
0.6364 Remote Similarity NPC94351
0.6364 Remote Similarity NPC168303
0.6304 Remote Similarity NPC10588
0.625 Remote Similarity NPC610566
0.617 Remote Similarity NPC72947
0.6087 Remote Similarity NPC166761
0.6047 Remote Similarity NPC470700
0.6047 Remote Similarity NPC54844
0.6047 Remote Similarity NPC39097
0.6047 Remote Similarity NPC302681
0.6047 Remote Similarity NPC118286
0.6047 Remote Similarity NPC109691
0.587 Remote Similarity NPC487736
0.587 Remote Similarity NPC196479
0.5778 Remote Similarity NPC39664
0.5652 Remote Similarity NPC55561
0.5625 Remote Similarity NPC129373
0.5577 Remote Similarity NPC248396
0.5532 Remote Similarity NPC232523
0.551 Remote Similarity NPC204901
0.5435 Remote Similarity NPC177420
0.5417 Remote Similarity NPC488413
0.5417 Remote Similarity NPC488412
0.5366 Remote Similarity NPC606762
0.5294 Remote Similarity NPC294741
0.5263 Remote Similarity NPC115188
0.5263 Remote Similarity NPC159760
0.5185 Remote Similarity NPC305603
0.5185 Remote Similarity NPC249836
0.5111 Remote Similarity NPC25493

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC210497 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
NPD

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