Natural Product: NPC222327

Natural Product IDNPC222327
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (1R,2S)-2-[(S)-Amino(Carboxy)Methyl]Cyclopropane-1-Carboxylic Acid
IUPAC Name (1R,2S)-2-[(S)-amino(carboxy)methyl]cyclopropane-1-carboxylic acid
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL285369
PubChem CID 5310957
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
                • [CHEMONTID:0004146] L-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 GZOVEPYOCJWRFC-NUNKFHFFSA-N
Standard InCHI InChI=1S/C6H9NO4/c7-4(6(10)11)2-1-3(2)5(8)9/h2-4H,1,7H2,(H,8,9)(H,10,11)/t2-,3+,4-/m0/s1
SMILES N[C@@H]([C@H]1C[C@H]1C(=O)O)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
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)98060-9]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1042/bst0160071]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[11559179]
NPO18777 Endiandra anthropophagorum Species Lauraceae Eukaryota n.a. Australian n.a. PMID[17583952]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[18001808]
NPO16051 Beilschmiedia erythrophloia Species Lauraceae Eukaryota Roots n.a. n.a. PMID[19072217]
NPO18777 Endiandra anthropophagorum Species Lauraceae Eukaryota n.a. Australian rainforest n.a. PMID[19138858]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[20954721]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[23479199]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[36500609]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4518.1 Saccharothrix mutabilis subsp. capreolus Subspecies Pseudonocardiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO16051 Beilschmiedia erythrophloia Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19179 Laminaria ochroleuca Species Laminariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17364 Engelhardtia chrysolepis n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO18503 Eugenia kurzii Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5074 Coryneum modonium n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9807 Fuscoporia gilva Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4518.1 Saccharothrix mutabilis subsp. capreolus Subspecies Pseudonocardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO19179 Laminaria ochroleuca Species Laminariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7424 Mitragyna javanica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12002 Amoora dasyclada n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16051 Beilschmiedia erythrophloia Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5074 Coryneum modonium n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO12637 Carpinus japonica Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18777 Endiandra anthropophagorum Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15019 Pteridium caudatum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13217 Helichrysum cameroonense Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17364 Engelhardtia chrysolepis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26440 Cedrela glaziovii Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18503 Eugenia kurzii Species Myrtaceae 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
NPT1519 Individual protein Excitatory amino acid transporter 2 Homo sapiens IC50 = 4000.0 nM PMID[20812729]
NPT1496 Protein complex Glutamate NMDA receptor Rattus norvegicus IC50 = 10000.0 nM PMID[1533422]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT2 Others Unspecified n.a. Potency n.a. 19952.6 nM PubChem BioAssay data set

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 NPC222327 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 NPC188231
0.5652 Remote Similarity NPC132307
0.5652 Remote Similarity NPC126925
0.56 Remote Similarity NPC84636
0.56 Remote Similarity NPC226027
0.56 Remote Similarity NPC174246
0.56 Remote Similarity NPC43204

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC222327 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
0.5652 Remote Similarity NPD8798 Phase 2
0.56 Remote Similarity NPD9017 Phase 2

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