Natural Product: NPC88898

Natural Product IDNPC88898
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (2S,4S)-4-Hydroxyglutamic Acid
IUPAC Name (2S,4S)-2-amino-4-hydroxypentanedioic acid
Synonyms (2S,4S)-4-Hydroxyglutamic Acid
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL197110
PubChem CID 192790
44286641
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:0004323] Glutamic acid and derivatives

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 HBDWQSHEVMSFGY-HRFVKAFMSA-N
Standard InCHI InChI=1S/C5H9NO5/c6-2(4(8)9)1-3(7)5(10)11/h2-3,7H,1,6H2,(H,8,9)(H,10,11)/t2-,3-/m0/s1
SMILES C([C@@H](C(=O)O)N)[C@@H](C(=O)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
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.lwt.2014.11.023]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae 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
NPT3080 Individual protein Metabotropic glutamate receptor 1 Rattus norvegicus EC50 = 11000.0 nM PMID[11412983]
NPT3081 Individual protein Metabotropic glutamate receptor 2 Rattus norvegicus EC50 = 137000.0 nM PMID[11412983]
NPT3080 Individual protein Metabotropic glutamate receptor 1 Rattus norvegicus Rmax = 95.0 mM PMID[11412983]
NPT3081 Individual protein Metabotropic glutamate receptor 2 Rattus norvegicus Rmax = 60.0 mM PMID[11412983]
NPT1520 Individual protein Excitatory amino acid transporter 1 Homo sapiens pKm = 4.06 n.a. PMID[16335922]
NPT1519 Individual protein Excitatory amino acid transporter 2 Homo sapiens pKm = 4.21 n.a. PMID[16335922]
NPT1518 Individual protein Excitatory amino acid transporter 3 Homo sapiens pKm = 4.16 n.a. PMID[16335922]
NPT4028 Individual protein Metabotropic glutamate receptor 8 Rattus norvegicus EC50 = 53000.0 nM PMID[11412983]
NPT4028 Individual protein Metabotropic glutamate receptor 8 Rattus norvegicus Rmax = 94.0 mM PMID[11412983]

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 NPC88898 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 NPC106216
0.6 Remote Similarity NPC43169
0.6 Remote Similarity NPC327895
0.6 Remote Similarity NPC112224
0.5769 Remote Similarity NPC49952
0.5769 Remote Similarity NPC136476
0.56 Remote Similarity NPC309658
0.5417 Remote Similarity NPC63621
0.5417 Remote Similarity NPC326992
0.5417 Remote Similarity NPC5505
0.5417 Remote Similarity NPC121517
0.5417 Remote Similarity NPC168375
0.5417 Remote Similarity NPC600066
0.52 Remote Similarity NPC226265
0.52 Remote Similarity NPC219143
0.52 Remote Similarity NPC254482
0.52 Remote Similarity NPC110533
0.5185 Remote Similarity NPC153370
0.5185 Remote Similarity NPC34908

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC88898 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
0.52 Remote Similarity NPD8215 Phase 4
0.52 Remote Similarity NPD8216 Phase 3
0.52 Remote Similarity NPD8217 Phase 3
0.5185 Remote Similarity NPD8614 Pre-clinical

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