Natural Product: NPC145885

Natural Product IDNPC145885
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 3-(1H-Indol-3-Yl)-2-(Trimethylazaniumyl)Propanoate
IUPAC Name 3-(1H-indol-3-yl)-2-(trimethylazaniumyl)propanoate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL448328
PubChem CID 3861164
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0002404] Alpha amino acids

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 AOHCBEAZXHZMOR-UHFFFAOYSA-N
Standard InCHI InChI=1S/C14H18N2O2/c1-16(2,3)13(14(17)18)8-10-9-15-12-7-5-4-6-11(10)12/h4-7,9,13,15H,8H2,1-3H3
SMILES C[N+](C)(C)C(Cc1c[nH]c2ccccc12)C(=O)[O-]

  Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. tuber n.a. PMID[12913245]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[1293938]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[16181762]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. root n.a. PMID[16564530]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota aerial parts n.a. n.a. PMID[19299148]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. stem n.a. PMID[22210168]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. leaf n.a. PMID[22210168]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[22223386]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota Lateral roots n.a. n.a. PMID[22607495]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[22628040]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[22907155]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[23225552]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[23707213]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[23707213]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[24793215]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota Leaves n.a. n.a. PMID[2691636]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[2691636]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[27761113]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota Roots n.a. n.a. PMID[29359942]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota Roots n.a. n.a. PMID[30892884]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota Roots n.a. n.a. PMID[31944695]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota Roots; Tubers n.a. n.a. PMID[7714535]
NPO7804 Desmodium gangeticum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20729 Aconitum coreanum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6792 Hedysarum polybotrys Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20729 Aconitum coreanum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7804 Desmodium gangeticum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20729 Aconitum coreanum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7804 Desmodium gangeticum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11452 Pterocarpus officinalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14905.1 Erythrina variegata var. orientalis Varieties Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7804 Desmodium gangeticum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6792 Hedysarum polybotrys Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6792 Hedysarum polybotrys Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11452 Pterocarpus officinalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20729 Aconitum coreanum Species Ranunculaceae 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
NPT3 Individual protein Thioredoxin glutathione reductase Schistosoma mansoni Potency = 50118.7 nM PubChem BioAssay data set
NPT60 Individual protein Lysosomal alpha-glucosidase Homo sapiens Potency = 28183.8 nM PubChem BioAssay data set
NPT59 Individual protein DNA polymerase beta Homo sapiens Potency = 7943.3 nM PubChem BioAssay data set
NPT49 Individual protein DNA-(apurinic or apyrimidinic site) lyase Homo sapiens Potency n.a. 25118.9 nM PubChem BioAssay data set

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT34 Cell line BV-2 Mus musculus IC50 > 100000.0 nM PMID[28911817]

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 NPC145885 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 NPC14113
1.0 High Similarity NPC84827
0.6136 Remote Similarity NPC601214
0.58 Remote Similarity NPC605863
0.5625 Remote Similarity NPC279081
0.5577 Remote Similarity NPC78020
0.5472 Remote Similarity NPC315555
0.5472 Remote Similarity NPC55772
0.5455 Remote Similarity NPC248041
0.5417 Remote Similarity NPC96102
0.54 Remote Similarity NPC84911
0.537 Remote Similarity NPC149155
0.537 Remote Similarity NPC203468
0.537 Remote Similarity NPC110500
0.537 Remote Similarity NPC605329
0.5306 Remote Similarity NPC230869
0.5273 Remote Similarity NPC480318
0.52 Remote Similarity NPC29886
0.5192 Remote Similarity NPC310665
0.5185 Remote Similarity NPC59269
0.5088 Remote Similarity NPC480317
0.5088 Remote Similarity NPC480316

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC145885 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
0.5417 Remote Similarity NPD198 Clinical (unspecified phase)
0.537 Remote Similarity NPD482 Phase 4
0.5273 Remote Similarity NPD749 Clinical (unspecified phase)

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