Natural Product: NPC118636

Natural Product IDNPC118636
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XQNPFRPIWBMLRN-ONEGZZNKSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10932638
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002341] Phenol ethers
        • [CHEMONTID:0000138] Anisoles

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 XQNPFRPIWBMLRN-ONEGZZNKSA-N
Standard InCHI InChI=1S/C12H14O3/c1-10(13)15-9-3-4-11-5-7-12(14-2)8-6-11/h3-8H,9H2,1-2H3/b4-3+
SMILES CC(=O)OC/C=C/c1ccc(cc1)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   206.09 Volume:   220.74
?
Van der Waals volume.
Dense:   0.934 LogP:   2.552
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.529
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.719
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   8.0
TPSA:   35.53
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   0.0 Rings:   1.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.709 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   1.873 Fsp3:   0.25
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:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.109 Fluc inhibitor:   0.699
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.044
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.367
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.998 Promiscuous compounds:   0.063

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.585 MDCK Permeability:   -4.488
Pgp-inhibitor:   0.986 Pgp-substrate:   0.013
PAMPA:   0.036
?
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):   0.161
20% Bioavailability (F20%):   0.779 30% Bioavailability (F30%):   0.928
50% Bioavailability (F50%):   0.89

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.008 MRP1:   0.002
Plasma Protein Binding (PPB):   85.877% Volume Distribution (VD):   0.091
Fu: 17.927%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.992
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.934
BSEP inhibitor:   0.998

ADMET: Metabolism

CYP1A2-inhibitor:   0.212 CYP1A2-substrate:   0.229
CYP2C19-inhibitor:   0.019 CYP2C19-substrate:   0.313
CYP2C9-inhibitor:   0.524 CYP2C9-substrate:   0.037
CYP2D6-inhibitor:   0.924 CYP2D6-substrate:   0.069
CYP3A4-inhibitor:   0.003 CYP3A4-substrate:   0.371
CYP2B6-substrate:   0.167 CYP2C8-inhibitor:   1.0
HLM stability:   0.703
?
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):  8.979 Half-life (T1/2):  0.438

ADMET: Toxicity

hERG Blockers:  0.192 hERG Blockers (10um):  0.461
Human Hepatotoxicity (H-HT):  0.409 Drug-induced Liver Injury (DILI):  0.664
AMES Toxicity:  0.783 Rat Oral Acute Toxicity:  0.08
Maximum Recommended Daily Dose:  0.245 Skin Sensitization:  0.658
Carcinogencity:  0.792 Eye Corrosion:  0.3
Eye Irritation:  0.972 Respiratory Toxicity:  0.262
Drug-induced Neurotoxicity:  0.461 Ototoxicity:  0.117
Hematotoxicity:  0.31 Drug-induced Nephrotoxicity:  0.293
Genotoxicity:  0.116 RPMI-8226 Immunitoxicity:  0.067
A549 Cytotoxicity:  0.021 Hek293 Cytotoxicity:  0.15
BCF:   1.179
?
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:   3.637
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.339
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.783
?
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
NPO14260 Euphorbia kansui Species Euphorbiaceae Eukaryota roots n.a. n.a. PMID[12350140]
NPO14260 Euphorbia kansui Species Euphorbiaceae Eukaryota Roots n.a. n.a. PMID[12762796]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. bark n.a. PMID[15283458]
NPO14260 Euphorbia kansui Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[15387657]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. stem n.a. PMID[15577257]
NPO14260 Euphorbia kansui Species Euphorbiaceae Eukaryota n.a. root n.a. PMID[1955882]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[38790803]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota Fruits n.a. n.a. PMID[8021657]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[9051910]
NPO5911 Anchusa officinalis Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6519 Calocera viscosa Species Dacrymycetaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13970 Caryopteris mongholica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10773 Dalbergia rubiginosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14260 Euphorbia kansui Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16626 Leucetta microrhaphis Species Leucettidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16137 Mappia foetida Species Icacinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12693 Mesembryanthemum tortuosum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7027 Metapenaeus macleayi Species Penaeidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13368 Monomorium delagoense Species Formicidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14465 Ramalina terebrata Species Ramalinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18379 Satureja atropatana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10551 Acanthopanax ricinifolius n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO13274 Illicium verum Species Schisandraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae 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 n.a. n.a. Database[FooDB]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO5911 Anchusa officinalis Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12693 Mesembryanthemum tortuosum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14260 Euphorbia kansui Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12693 Mesembryanthemum tortuosum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5911 Anchusa officinalis Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14260 Euphorbia kansui Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14260 Euphorbia kansui Species Euphorbiaceae 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]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14260 Euphorbia kansui Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5911 Anchusa officinalis Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13970 Caryopteris mongholica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14260 Euphorbia kansui Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10551 Acanthopanax ricinifolius n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO14465 Ramalina terebrata Species Ramalinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12693 Mesembryanthemum tortuosum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16137 Mappia foetida Species Icacinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18379 Satureja atropatana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8896 Anacardium occidentale Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16626 Leucetta microrhaphis Species Leucettidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7027 Metapenaeus macleayi Species Penaeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6519 Calocera viscosa Species Dacrymycetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13368 Monomorium delagoense Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10773 Dalbergia rubiginosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13274 Illicium verum Species Schisandraceae 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

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 NPC118636 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
0.8 Intermediate Similarity NPC283546
0.7838 Intermediate Similarity NPC94347
0.6744 Remote Similarity NPC126220
0.6579 Remote Similarity NPC179686
0.6571 Remote Similarity NPC175393
0.6364 Remote Similarity NPC99886
0.6364 Remote Similarity NPC259134
0.6364 Remote Similarity NPC8002
0.6279 Remote Similarity NPC38403
0.6087 Remote Similarity NPC159916
0.5897 Remote Similarity NPC171843
0.5833 Remote Similarity NPC175298
0.5652 Remote Similarity NPC277460
0.5556 Remote Similarity NPC13755
0.551 Remote Similarity NPC237131
0.5417 Remote Similarity NPC326447
0.5263 Remote Similarity NPC4718

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC118636 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
0.5814 Remote Similarity NPD1358 Phase 4
0.5417 Remote Similarity NPD3134 Approved

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