Natural Product: NPC150624

Natural Product IDNPC150624
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Batatasin Iv
IUPAC Name 3-[2-(2-hydroxyphenyl)ethyl]-5-methoxyphenol
Synonyms Batatasin Iv
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL228126
PubChem CID 181271
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000253] Stilbenes

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 IUMFLNFLJUUODE-UHFFFAOYSA-N
Standard InCHI InChI=1S/C15H16O3/c1-18-14-9-11(8-13(16)10-14)6-7-12-4-2-3-5-15(12)17/h2-5,8-10,16-17H,6-7H2,1H3
SMILES COc1cc(CCc2ccccc2O)cc(c1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   244.11 Volume:   261.435
?
Van der Waals volume.
Dense:   0.934 LogP:   3.956
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.559
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.504
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   12.0
TPSA:   49.69
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   2.0 Rings:   2.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.869 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   1.943 Fsp3:   0.2
MCE-18:   11.0
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.279 Fluc inhibitor:   0.1
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.045
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.324
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.857 Promiscuous compounds:   0.317

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.861 MDCK Permeability:   -4.764
Pgp-inhibitor:   0.007 Pgp-substrate:   0.005
PAMPA:   0.278
?
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):   0.034
20% Bioavailability (F20%):   0.894 30% Bioavailability (F30%):   0.897
50% Bioavailability (F50%):   0.964

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.021 MRP1:   0.328
Plasma Protein Binding (PPB):   88.725% Volume Distribution (VD):   0.276
Fu: 11.395%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.989
OATP1B3 inhibitor:   0.984 BCRP inhibitor:   0.015
BSEP inhibitor:   0.731

ADMET: Metabolism

CYP1A2-inhibitor:   1.0 CYP1A2-substrate:   0.989
CYP2C19-inhibitor:   0.975 CYP2C19-substrate:   0.916
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.998
CYP2D6-inhibitor:   0.999 CYP2D6-substrate:   0.917
CYP3A4-inhibitor:   0.373 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.607 CYP2C8-inhibitor:   1.0
HLM stability:   0.982
?
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):  11.368 Half-life (T1/2):  0.922

ADMET: Toxicity

hERG Blockers:  0.401 hERG Blockers (10um):  0.823
Human Hepatotoxicity (H-HT):  0.578 Drug-induced Liver Injury (DILI):  0.066
AMES Toxicity:  0.515 Rat Oral Acute Toxicity:  0.148
Maximum Recommended Daily Dose:  0.542 Skin Sensitization:  0.868
Carcinogencity:  0.215 Eye Corrosion:  0.463
Eye Irritation:  0.972 Respiratory Toxicity:  0.691
Drug-induced Neurotoxicity:  0.245 Ototoxicity:  0.351
Hematotoxicity:  0.157 Drug-induced Nephrotoxicity:  0.425
Genotoxicity:  0.167 RPMI-8226 Immunitoxicity:  0.095
A549 Cytotoxicity:  0.532 Hek293 Cytotoxicity:  0.711
BCF:   1.439
?
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:   3.96
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.102
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.542
?
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
NPO809 Leitneria floridana Species Simaroubaceae Eukaryota n.a. aerial part n.a. PMID[11141127]
NPO20097 Thermobifida alba Species Nocardiopsaceae Bacteria n.a. n.a. n.a. PMID[11430001]
NPO27517 Crinum latifolium Species Amaryllidaceae Eukaryota n.a. leaf n.a. PMID[15595606]
NPO7863 Dioscorea opposita Species Dioscoreaceae Eukaryota aerial parts n.a. n.a. PMID[16124773]
NPO5635 Bauhinia purpurea Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16562827]
NPO5635 Bauhinia purpurea Species Fabaceae Eukaryota roots Phitsanulok Province, Thailand 2004-MAY PMID[17480099]
NPO5635 Bauhinia purpurea Species Fabaceae Eukaryota n.a. root n.a. PMID[17480099]
NPO1103 Dioscorea japonica Species Dioscoreaceae Eukaryota rhizomes n.a. n.a. PMID[21353549]
NPO24833 Dioscorea polystachya Species Dioscoreaceae Eukaryota n.a. bark n.a. PMID[24689699]
NPO9419 Enterobacter cloacae Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[25427277]
NPO24359 Streptomyces cacaoi Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[27642865]
NPO26245 Styracaster caroli Species Porcellanasteridae Eukaryota n.a. n.a. n.a. PMID[8145229]
NPO24359 Streptomyces cacaoi Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO27517 Crinum latifolium Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13147 Euphorbia cyparissias Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1103 Dioscorea japonica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7863 Dioscorea opposita Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3357 Alnus cordata Species Betulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4628 Aloe deltoideodonta Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5635 Bauhinia purpurea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4382 Elmerrillia papuana n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO1490 Goldfussia yunnanensis n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO8807 Laurentia longiflora n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO809 Leitneria floridana Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8559 Calophyllum venulosum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11319 Laurencia hybrida Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26245 Styracaster caroli Species Porcellanasteridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2692 Dioscorea rotundata Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2455 Thermopsis mollis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25475 Syphonota geographica Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6828 Purpura aperta Species Muricidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9881 Petrosia hebes Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8977 Notholaena aschenborniana Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20097 Thermobifida alba Species Nocardiopsaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO9419 Enterobacter cloacae Species Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO9608 Lepraria citrina Species Stereocaulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27517 Crinum latifolium Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2692 Dioscorea rotundata Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1103 Dioscorea japonica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24833 Dioscorea polystachya Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27517 Crinum latifolium Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1103 Dioscorea japonica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2692 Dioscorea rotundata Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7863 Dioscorea opposita Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24833 Dioscorea polystachya Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7863 Dioscorea opposita Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1103 Dioscorea japonica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7863 Dioscorea opposita Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19605 Tara spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6054 Sinularia brongersmai Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9881 Petrosia hebes Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1103 Dioscorea japonica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4628 Aloe deltoideodonta Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8977 Notholaena aschenborniana Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3357 Alnus cordata Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2455 Thermopsis mollis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6828 Purpura aperta Species Muricidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9608 Lepraria citrina Species Stereocaulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO809 Leitneria floridana Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8807 Laurentia longiflora n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO4382 Elmerrillia papuana n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO25475 Syphonota geographica Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5635 Bauhinia purpurea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26245 Styracaster caroli Species Porcellanasteridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13147 Euphorbia cyparissias Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10024 Tylecodon wallichii Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8559 Calophyllum venulosum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27517 Crinum latifolium Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11319 Laurencia hybrida Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6962 Cetraria delisei Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11181 Juniperus bermudiana Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24833 Dioscorea polystachya Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8460 Pedicularis torta Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20097 Thermobifida alba Species Nocardiopsaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO1490 Goldfussia yunnanensis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO24359 Streptomyces cacaoi Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2692 Dioscorea rotundata Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9419 Enterobacter cloacae Species Enterobacteriaceae Bacteria 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
NPT30 Individual protein Cyclooxygenase-1 Homo sapiens IC50 > 40900.0 nM PMID[17480099]
NPT31 Individual protein Cyclooxygenase-2 Homo sapiens IC50 > 40900.0 nM PMID[17480099]
NPT324 Individual protein Cyclooxygenase-1 Ovis aries IC50 > 100.0 ug.mL-1 PMID[19303782]
NPT325 Individual protein Cyclooxygenase-2 Ovis aries IC50 > 100.0 ug.mL-1 PMID[19303782]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT91 Cell line KB Homo sapiens IC50 > 81800.0 nM PMID[17480099]
NPT76 Cell line C6 Rattus norvegicus Activity = 106.1 % PMID[21353549]
NPT76 Cell line C6 Rattus norvegicus Activity = 95.0 % PMID[21353549]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 > 81800.0 nM PMID[17480099]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC = 204600.0 nM PMID[17480099]
NPT20 Organism Candida albicans Candida albicans IC50 > 204600.0 nM PMID[17480099]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 100.0 ug.mL-1 PMID[19303782]
NPT1 Others Radical scavenging activity n.a. IC50 > 100.0 ug.mL-1 PMID[19303782]

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 NPC150624 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
0.7317 Intermediate Similarity NPC276737
0.7143 Intermediate Similarity NPC69261
0.7143 Intermediate Similarity NPC22610
0.6905 Remote Similarity NPC141090
0.6591 Remote Similarity NPC53906
0.6522 Remote Similarity NPC246620
0.6522 Remote Similarity NPC184302
0.6383 Remote Similarity NPC33270
0.6364 Remote Similarity NPC105925
0.6364 Remote Similarity NPC293054
0.6304 Remote Similarity NPC117214
0.6087 Remote Similarity NPC282496
0.6087 Remote Similarity NPC116907
0.5952 Remote Similarity NPC102216
0.5745 Remote Similarity NPC266691
0.5625 Remote Similarity NPC28765
0.549 Remote Similarity NPC63574
0.5106 Remote Similarity NPC168657
0.5088 Remote Similarity NPC603965

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC150624 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