Natural Product: NPC302219

Natural Product IDNPC302219
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}Resorcinol
IUPAC Name 5-[(8Z,11Z)-pentadeca-8,11-dienyl]benzene-1,3-diol
Synonyms 5-{8(Z),11(Z)-Pentadecadienyl}Resorcinol
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL459604
PubChem CID 11702450
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000134] Phenols
        • [CHEMONTID:0001286] Benzenediols
          • [CHEMONTID:0000137] Resorcinols

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 UFMJCOLGRWKUKO-UTOQUPLUSA-N
Standard InCHI InChI=1S/C21H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-19-16-20(22)18-21(23)17-19/h4-5,7-8,16-18,22-23H,2-3,6,9-15H2,1H3/b5-4-,8-7-
SMILES CCC/C=CC/C=CCCCCCCCc1cc(O)cc(c1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   316.24 Volume:   367.614
?
Van der Waals volume.
Dense:   0.86 LogP:   7.975
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.761
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.428
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   12.0 Rigid Bonds:   8.0
TPSA:   40.46
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   2.0 Rings:   1.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.352 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.564 Fsp3:   0.524
MCE-18:   6.0
?
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:   0.697 Fluc inhibitor:   0.331
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.104
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.935 Promiscuous compounds:   0.093

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.2 MDCK Permeability:   -4.819
Pgp-inhibitor:   0.179 Pgp-substrate:   0.002
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):   0.0
20% Bioavailability (F20%):   0.793 30% Bioavailability (F30%):   0.909
50% Bioavailability (F50%):   0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.036 MRP1:   0.973
Plasma Protein Binding (PPB):   98.941% Volume Distribution (VD):   0.562
Fu: 0.659%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.302
OATP1B3 inhibitor:   0.823 BCRP inhibitor:   0.678
BSEP inhibitor:   0.964

ADMET: Metabolism

CYP1A2-inhibitor:   0.089 CYP1A2-substrate:   0.997
CYP2C19-inhibitor:   0.726 CYP2C19-substrate:   0.985
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.955
CYP2D6-inhibitor:   0.889 CYP2D6-substrate:   1.0
CYP3A4-inhibitor:   0.002 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.43 CYP2C8-inhibitor:   1.0
HLM stability:   0.753
?
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):  5.236 Half-life (T1/2):  0.704

ADMET: Toxicity

hERG Blockers:  0.683 hERG Blockers (10um):  0.863
Human Hepatotoxicity (H-HT):  0.218 Drug-induced Liver Injury (DILI):  0.0
AMES Toxicity:  0.39 Rat Oral Acute Toxicity:  0.037
Maximum Recommended Daily Dose:  0.042 Skin Sensitization:  1.0
Carcinogencity:  0.009 Eye Corrosion:  1.0
Eye Irritation:  1.0 Respiratory Toxicity:  0.878
Drug-induced Neurotoxicity:  0.037 Ototoxicity:  0.075
Hematotoxicity:  0.0 Drug-induced Nephrotoxicity:  0.221
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.05
A549 Cytotoxicity:  0.932 Hek293 Cytotoxicity:  0.489
BCF:   1.658
?
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:   4.919
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.009
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.601
?
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
NPO25294 Merulius incarnatus Species Meruliaceae Eukaryota n.a. n.a. n.a. PMID[16643059]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota Fruits n.a. n.a. PMID[8021657]
NPO25294 Merulius incarnatus Species Meruliaceae 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]
NPO13016 Viscaria viscosa Species Caryophyllaceae 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]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3580 Rana amurensis Species Ranidae 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]
NPO25294 Merulius incarnatus Species Meruliaceae 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 = 167000.0 nM DOI[10.1021/np50114a025]
NPT43 Individual protein Tyrosinase Agaricus bisporus Inhibition = 89.0 % PMID[8021657]
NPT43 Individual protein Tyrosinase Agaricus bisporus ID50 = 0.05 mM PMID[8021657]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IC50 = 5.0 ug.mL-1 PMID[16643059]
NPT85 Organism Filobasidiella neoformans Cryptococcus neoformans IC50 = 20.0 ug.mL-1 PMID[16643059]

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 NPC302219 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
0.9459 High Similarity NPC71002
0.9459 High Similarity NPC249828
0.8947 High Similarity NPC242342
0.8947 High Similarity NPC85479
0.8889 High Similarity NPC53051
0.8889 High Similarity NPC24404
0.8889 High Similarity NPC313030
0.8649 High Similarity NPC146798
0.8649 High Similarity NPC222522
0.8649 High Similarity NPC106396
0.8649 High Similarity NPC94351
0.8649 High Similarity NPC168303
0.8462 Intermediate Similarity NPC10588
0.8333 Intermediate Similarity NPC470700
0.8333 Intermediate Similarity NPC54844
0.8333 Intermediate Similarity NPC39097
0.8333 Intermediate Similarity NPC302681
0.8333 Intermediate Similarity NPC118286
0.8333 Intermediate Similarity NPC109691
0.825 Intermediate Similarity NPC72947
0.8205 Intermediate Similarity NPC166761
0.7895 Intermediate Similarity NPC39664
0.7442 Intermediate Similarity NPC210497
0.7381 Intermediate Similarity NPC158253
0.7027 Intermediate Similarity NPC294186
0.7027 Intermediate Similarity NPC147310
0.7027 Intermediate Similarity NPC137415
0.7027 Intermediate Similarity NPC166313
0.7027 Intermediate Similarity NPC192032
0.7027 Intermediate Similarity NPC24407
0.7027 Intermediate Similarity NPC11280
0.6809 Remote Similarity NPC305603
0.6744 Remote Similarity NPC284011
0.6667 Remote Similarity NPC246056
0.6512 Remote Similarity NPC483454
0.6512 Remote Similarity NPC162314
0.6458 Remote Similarity NPC61033
0.6364 Remote Similarity NPC94139
0.6364 Remote Similarity NPC147284
0.6304 Remote Similarity NPC48730
0.6304 Remote Similarity NPC192
0.6279 Remote Similarity NPC232523
0.6275 Remote Similarity NPC140521
0.6222 Remote Similarity NPC204901
0.6136 Remote Similarity NPC488413
0.6136 Remote Similarity NPC488412
0.6122 Remote Similarity NPC127894
0.6122 Remote Similarity NPC470759
0.5962 Remote Similarity NPC123559
0.5909 Remote Similarity NPC487734
0.5909 Remote Similarity NPC486908
0.5714 Remote Similarity NPC241891
0.5714 Remote Similarity NPC134829
0.5714 Remote Similarity NPC470760
0.5581 Remote Similarity NPC487946
0.5581 Remote Similarity NPC487945
0.551 Remote Similarity NPC483450
0.549 Remote Similarity NPC249836
0.5333 Remote Similarity NPC55561
0.5319 Remote Similarity NPC129373
0.5319 Remote Similarity NPC488416
0.5306 Remote Similarity NPC219070
0.5306 Remote Similarity NPC483449
0.5294 Remote Similarity NPC248396
0.5217 Remote Similarity NPC196479
0.5111 Remote Similarity NPC177420

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC302219 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