Natural Product: NPC137415

Natural Product IDNPC137415
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 5-Tridecyl Resorcinol
IUPAC Name 5-tridecylbenzene-1,3-diol
Synonyms 5-Tridecyl Resorcinol; 6-Tridecylresorcylic Acid
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL451044
PubChem CID 174862
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 UXOGOSLLGMYCNL-UHFFFAOYSA-N
Standard InCHI InChI=1S/C19H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-17-14-18(20)16-19(21)15-17/h14-16,20-21H,2-13H2,1H3
SMILES CCCCCCCCCCCCCc1cc(O)cc(c1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   292.24 Volume:   338.295
?
Van der Waals volume.
Dense:   0.864 LogP:   7.817
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.561
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.784
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   12.0 Rigid Bonds:   6.0
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:   0.467 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.013 Fsp3:   0.684
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:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.718 Fluc inhibitor:   0.362
?
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:   0.013
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.962 Promiscuous compounds:   0.109

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.204 MDCK Permeability:   -4.815
Pgp-inhibitor:   0.005 Pgp-substrate:   0.029
PAMPA:   0.002
?
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%):   0.931 30% Bioavailability (F30%):   0.974
50% Bioavailability (F50%):   0.989

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.097 MRP1:   0.783
Plasma Protein Binding (PPB):   100.037% Volume Distribution (VD):   1.467
Fu: 0.822%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.84
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.826
BSEP inhibitor:   0.465

ADMET: Metabolism

CYP1A2-inhibitor:   0.111 CYP1A2-substrate:   0.998
CYP2C19-inhibitor:   0.297 CYP2C19-substrate:   0.975
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.998
CYP2D6-inhibitor:   0.997 CYP2D6-substrate:   0.949
CYP3A4-inhibitor:   0.008 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.826 CYP2C8-inhibitor:   1.0
HLM stability:   0.42
?
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):  4.289 Half-life (T1/2):  1.098

ADMET: Toxicity

hERG Blockers:  0.669 hERG Blockers (10um):  0.899
Human Hepatotoxicity (H-HT):  0.487 Drug-induced Liver Injury (DILI):  0.085
AMES Toxicity:  0.117 Rat Oral Acute Toxicity:  0.22
Maximum Recommended Daily Dose:  0.545 Skin Sensitization:  0.977
Carcinogencity:  0.246 Eye Corrosion:  0.959
Eye Irritation:  0.998 Respiratory Toxicity:  0.911
Drug-induced Neurotoxicity:  0.082 Ototoxicity:  0.15
Hematotoxicity:  0.073 Drug-induced Nephrotoxicity:  0.09
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.05
A549 Cytotoxicity:  0.843 Hek293 Cytotoxicity:  0.725
BCF:   1.372
?
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:   5.084
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.928
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.855
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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
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Leaves n.a. n.a. PMID[27140807]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota leaves n.a. n.a. PMID[33127538]
NPO22588 Lysimachia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. PMID[6090589]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota fresh sarcotestas Kwanak Campus of Seoul National University, Seoul, Korea 1996-Sep PMID[9677265]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota leaves St. Louis 1996-SEP PMID[9834151]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. PMID[9834158]
NPO22588 Lysimachia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota Wood n.a. n.a. Database[FooDB]
NPO29719 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22588 Lysimachia japonica Species Primulaceae 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
NPT324 Individual protein Cyclooxygenase-1 Ovis aries IC50 = 2380.0 nM PMID[32738413]
NPT31 Individual protein Cyclooxygenase-2 Homo sapiens IC50 = 2740.0 nM PMID[32738413]
NPT657 Individual protein 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-1 Bos taurus IC50 = 72320.0 nM PMID[15270567]
NPT570 Individual protein Arachidonate 5-lipoxygenase Homo sapiens Inhibition < 50.0 % PMID[32738413]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT83 Cell line MCF7 Homo sapiens IC50 = 1.91 ug.mL-1 PMID[17502416]
NPT658 Cell line HT1197 Homo sapiens IC50 = 2.2 ug.mL-1 PMID[17502416]
NPT148 Cell line HCT-15 Homo sapiens IC50 = 15.32 ug.mL-1 PMID[17502416]
NPT81 Cell line A549 Homo sapiens IC50 > 50.0 ug.mL-1 PMID[17502416]
NPT146 Cell line SK-OV-3 Homo sapiens IC50 > 50.0 ug.mL-1 PMID[17502416]
NPT2 Others Unspecified n.a. IC50 = 8000.0 nM PMID[22037378]

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 NPC137415 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
1.0 High Similarity NPC294186
1.0 High Similarity NPC147310
1.0 High Similarity NPC166313
1.0 High Similarity NPC192032
1.0 High Similarity NPC24407
1.0 High Similarity NPC11280
0.8889 High Similarity NPC246056
0.8182 Intermediate Similarity NPC146798
0.8182 Intermediate Similarity NPC222522
0.8182 Intermediate Similarity NPC106396
0.8182 Intermediate Similarity NPC94351
0.8182 Intermediate Similarity NPC168303
0.7941 Intermediate Similarity NPC486908
0.7879 Intermediate Similarity NPC53051
0.7879 Intermediate Similarity NPC24404
0.7879 Intermediate Similarity NPC313030
0.75 Intermediate Similarity NPC71002
0.75 Intermediate Similarity NPC249828
0.7273 Intermediate Similarity NPC470700
0.7273 Intermediate Similarity NPC54844
0.7273 Intermediate Similarity NPC39097
0.7273 Intermediate Similarity NPC302681
0.7273 Intermediate Similarity NPC241891
0.7273 Intermediate Similarity NPC118286
0.7273 Intermediate Similarity NPC134829
0.7273 Intermediate Similarity NPC109691
0.7027 Intermediate Similarity NPC302219
0.6857 Remote Similarity NPC39664
0.6765 Remote Similarity NPC3358
0.6765 Remote Similarity NPC306884
0.6765 Remote Similarity NPC603092
0.6667 Remote Similarity NPC59506
0.6579 Remote Similarity NPC242342
0.6579 Remote Similarity NPC85479
0.6471 Remote Similarity NPC488411
0.6471 Remote Similarity NPC488410
0.6471 Remote Similarity NPC488409
0.6429 Remote Similarity NPC486909
0.6364 Remote Similarity NPC123273
0.6364 Remote Similarity NPC318325
0.6316 Remote Similarity NPC166761
0.6279 Remote Similarity NPC305603
0.6176 Remote Similarity NPC37802
0.6154 Remote Similarity NPC10588
0.6154 Remote Similarity NPC284011
0.6 Remote Similarity NPC114064
0.6 Remote Similarity NPC72947
0.575 Remote Similarity NPC94139
0.575 Remote Similarity NPC147284
0.5745 Remote Similarity NPC123559
0.5714 Remote Similarity NPC244513
0.5641 Remote Similarity NPC232523
0.5556 Remote Similarity NPC61033
0.5526 Remote Similarity NPC162113
0.5526 Remote Similarity NPC62546
0.55 Remote Similarity NPC488413
0.55 Remote Similarity NPC473691
0.55 Remote Similarity NPC483454
0.55 Remote Similarity NPC477454
0.55 Remote Similarity NPC162314
0.55 Remote Similarity NPC488415
0.55 Remote Similarity NPC488414
0.55 Remote Similarity NPC488412
0.5405 Remote Similarity NPC76938
0.5405 Remote Similarity NPC32714
0.5366 Remote Similarity NPC115808
0.5366 Remote Similarity NPC135414
0.5294 Remote Similarity NPC242240
0.5263 Remote Similarity NPC487946
0.5263 Remote Similarity NPC487945
0.5217 Remote Similarity NPC127894
0.5217 Remote Similarity NPC470759
0.5152 Remote Similarity NPC210849
0.5143 Remote Similarity NPC610566
0.5102 Remote Similarity NPC140521

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC137415 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
0.5135 Remote Similarity NPD846 Phase 4

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