Natural Product: NPC241891

Natural Product IDNPC241891
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 5-(10'-Phenyldecyl)-Resorcinol
IUPAC Name 5-(10-phenyldecyl)benzene-1,3-diol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL479019
PubChem CID 44575634
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 DOAKROJPUDWPEL-UHFFFAOYSA-N
Standard InCHI InChI=1S/C22H30O2/c23-21-16-20(17-22(24)18-21)15-9-6-4-2-1-3-5-8-12-19-13-10-7-11-14-19/h7,10-11,13-14,16-18,23-24H,1-6,8-9,12,15H2
SMILES C(CCCCCc1cc(cc(c1)O)O)CCCCc1ccccc1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   326.22 Volume:   373.717
?
Van der Waals volume.
Dense:   0.873 LogP:   5.772
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.752
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.478
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   11.0 Rigid Bonds:   12.0
TPSA:   40.46
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   2.0 Rings:   2.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.497 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   1.916 Fsp3:   0.455
MCE-18:   10.0
?
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:   0.838 Fluc inhibitor:   0.647
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.006
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.11
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.714 Promiscuous compounds:   0.069

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.202 MDCK Permeability:   -4.729
Pgp-inhibitor:   0.6 Pgp-substrate:   0.015
PAMPA:   0.011
?
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):   0.003
20% Bioavailability (F20%):   0.723 30% Bioavailability (F30%):   0.957
50% Bioavailability (F50%):   0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.278 MRP1:   0.392
Plasma Protein Binding (PPB):   100.536% Volume Distribution (VD):   1.19
Fu: 0.11%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.968
OATP1B3 inhibitor:   0.99 BCRP inhibitor:   0.699
BSEP inhibitor:   0.983

ADMET: Metabolism

CYP1A2-inhibitor:   0.697 CYP1A2-substrate:   0.998
CYP2C19-inhibitor:   0.359 CYP2C19-substrate:   0.99
CYP2C9-inhibitor:   0.997 CYP2C9-substrate:   0.999
CYP2D6-inhibitor:   0.95 CYP2D6-substrate:   0.894
CYP3A4-inhibitor:   0.286 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.293 CYP2C8-inhibitor:   1.0
HLM stability:   0.881
?
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):  3.794 Half-life (T1/2):  0.989

ADMET: Toxicity

hERG Blockers:  0.824 hERG Blockers (10um):  0.931
Human Hepatotoxicity (H-HT):  0.563 Drug-induced Liver Injury (DILI):  0.092
AMES Toxicity:  0.168 Rat Oral Acute Toxicity:  0.169
Maximum Recommended Daily Dose:  0.561 Skin Sensitization:  0.98
Carcinogencity:  0.148 Eye Corrosion:  0.77
Eye Irritation:  0.997 Respiratory Toxicity:  0.795
Drug-induced Neurotoxicity:  0.201 Ototoxicity:  0.154
Hematotoxicity:  0.054 Drug-induced Nephrotoxicity:  0.157
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.049
A549 Cytotoxicity:  0.818 Hek293 Cytotoxicity:  0.872
BCF:   1.528
?
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:   5.011
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.088
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.078
?
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
NPO11253 Knema glomerata Species Myristicaceae Eukaryota n.a. n.a. n.a. PMID[8201311]
NPO9687 Evernia esorediosa Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1623 Acarospora gobiensis Species Acarosporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10974 Acarus immobilis Species Acaridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2600 Alicyclobacillus acidoterrestris Species Alicyclobacillaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO7911 Bignonia gracilis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4339 Carthamus oxyacanthus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7774 Cliona copiosa Species Clionaidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4632 Crataegus pyracantha Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO987 Cruciata taurica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4957 Epimedium brevicornu Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6734 Gladiolus atroviolaceus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO561 Lindsaea chienii Species Lindsaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11121 Myrothamnus flabellifolia Species Myrothamnaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11344 Pilea cavaleriei Species Urticaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7502 Salpa thompsoni Species Salpidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12319 Xanthogaleruca luteola Species Chrysomelidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10410 Zephyranthes andersoniana Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4957 Epimedium brevicornu Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4957 Epimedium brevicornu Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO987 Cruciata taurica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10974 Acarus immobilis Species Acaridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11121 Myrothamnus flabellifolia Species Myrothamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2600 Alicyclobacillus acidoterrestris Species Alicyclobacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO7774 Cliona copiosa Species Clionaidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9687 Evernia esorediosa Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1623 Acarospora gobiensis Species Acarosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11344 Pilea cavaleriei Species Urticaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6734 Gladiolus atroviolaceus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10410 Zephyranthes andersoniana Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12319 Xanthogaleruca luteola Species Chrysomelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4632 Crataegus pyracantha Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4339 Carthamus oxyacanthus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4957 Epimedium brevicornu Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7911 Bignonia gracilis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7502 Salpa thompsoni Species Salpidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO561 Lindsaea chienii Species Lindsaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11253 Knema glomerata Species Myristicaceae 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
NPT81 Cell line A549 Homo sapiens ED50 = 3.49 ug ml-1 PMID[8201311]
NPT83 Cell line MCF7 Homo sapiens ED50 = 2.69 ug ml-1 PMID[8201311]
NPT139 Cell line HT-29 Homo sapiens ED50 = 3.24 ug ml-1 PMID[8201311]
NPT141 Organism Agrobacterium tumefaciens Agrobacterium tumefaciens T/C = 62.0 % PMID[8201311]

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
- Artemia LC50 = 0.47 ug.mL-1 PMID[8201311]

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 NPC241891 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 NPC134829
0.8 Intermediate Similarity NPC246056
0.7647 Intermediate Similarity NPC76938
0.7647 Intermediate Similarity NPC32714
0.7273 Intermediate Similarity NPC294186
0.7273 Intermediate Similarity NPC147310
0.7273 Intermediate Similarity NPC137415
0.7273 Intermediate Similarity NPC166313
0.7273 Intermediate Similarity NPC192032
0.7273 Intermediate Similarity NPC24407
0.7273 Intermediate Similarity NPC11280
0.6667 Remote Similarity NPC470700
0.6667 Remote Similarity NPC54844
0.6667 Remote Similarity NPC39097
0.6667 Remote Similarity NPC302681
0.6667 Remote Similarity NPC118286
0.6667 Remote Similarity NPC109691
0.6316 Remote Similarity NPC53051
0.6316 Remote Similarity NPC24404
0.6316 Remote Similarity NPC313030
0.6316 Remote Similarity NPC39664
0.6216 Remote Similarity NPC3358
0.6216 Remote Similarity NPC306884
0.6216 Remote Similarity NPC603092
0.6154 Remote Similarity NPC146798
0.6154 Remote Similarity NPC222522
0.6154 Remote Similarity NPC106396
0.6154 Remote Similarity NPC94351
0.6154 Remote Similarity NPC168303
0.6136 Remote Similarity NPC259942
0.6136 Remote Similarity NPC92624
0.6061 Remote Similarity NPC210849
0.6 Remote Similarity NPC486908
0.5882 Remote Similarity NPC100340
0.5714 Remote Similarity NPC71002
0.5714 Remote Similarity NPC10588
0.5714 Remote Similarity NPC302219
0.5714 Remote Similarity NPC242342
0.5714 Remote Similarity NPC249828
0.5714 Remote Similarity NPC85479
0.5714 Remote Similarity NPC284011
0.5682 Remote Similarity NPC294741
0.5581 Remote Similarity NPC114064
0.5581 Remote Similarity NPC72947
0.5556 Remote Similarity NPC606008
0.5476 Remote Similarity NPC483454
0.5476 Remote Similarity NPC162314
0.5405 Remote Similarity NPC123273
0.5405 Remote Similarity NPC318325
0.5349 Remote Similarity NPC94139
0.5349 Remote Similarity NPC147284
0.5135 Remote Similarity NPC610566
0.5122 Remote Similarity NPC474839
0.5111 Remote Similarity NPC188814
0.5111 Remote Similarity NPC608141

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC241891 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