Natural Product: NPC38473

Natural Product IDNPC38473
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Salvianolic Acid A
IUPAC Name (2R)-3-(3,4-dihydroxyphenyl)-2-[(E)-3-[2-[(E)-2-(3,4-dihydroxyphenyl)ethenyl]-3,4-dihydroxyphenyl]prop-2-enoyl]oxypropanoic acid
Synonyms Salvianolic Acid A
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL457077
PubChem CID 5281793
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 YMGFTDKNIWPMGF-UCPJVGPRSA-N
Standard InCHI InChI=1S/C26H22O10/c27-18-7-2-14(11-21(18)30)1-6-17-16(4-9-20(29)25(17)33)5-10-24(32)36-23(26(34)35)13-15-3-8-19(28)22(31)12-15/h1-12,23,27-31,33H,13H2,(H,34,35)/b6-1+,10-5+/t23-/m1/s1
SMILES O=C(O[C@@H](C(=O)O)Cc1ccc(c(c1)O)O)/C=C/c1ccc(c(c1/C=C/c1ccc(c(c1)O)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
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[ 17014425]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/bab.1236]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.indcrop.2010.09.006]
NPO9625 Salvia tomentosa Species Lamiaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/np50003a002]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[11374966]
NPO24054 Tournefortia sarmentosa Species Heliotropiaceae Eukaryota n.a. n.a. n.a. PMID[12027757]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[16038550]
NPO21056 Angelica keiskei Species Apiaceae Eukaryota exudates n.a. n.a. PMID[16441065]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17583950]
NPO21056 Angelica keiskei Species Apiaceae Eukaryota stems n.a. n.a. PMID[18558745]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[18855446]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20455578]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21775156]
NPO21056 Angelica keiskei Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21824777]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23286284]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[24108414]
NPO21056 Angelica keiskei Species Apiaceae Eukaryota stems n.a. n.a. PMID[25891102]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[27569393]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29185738]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30351923]
NPO29255 Salvia chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30370766]
NPO59850 Mentha cervina Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30792999]
NPO49209 Thymus pulegioides Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[35164249]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[3655791]
NPO16926 Thymbra capitata Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36557924]
NPO55161 Thymus alpestris Genus Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36829949]
NPO53896 Thymus glabrescens Genus Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36829949]
NPO61275 Thymus panonicus Genus Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36829949]
NPO63798 Thymus pulcherimus Genus Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36829949]
NPO49209 Thymus pulegioides Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36829949]
NPO16926 Thymbra capitata Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37111149]
NPO59850 Mentha cervina Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37570937]
NPO9625 Salvia tomentosa Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38338335]
NPO18048 Phlomis crinita Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[39419301]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota roots n.a. n.a. PMID[9834151]
NPO21056 Angelica keiskei Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9625 Salvia tomentosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24054 Tournefortia sarmentosa Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21396 Spongia vermicularis Species Spongiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19148 Gouania tomentosa Species Gobiesocidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29255 Salvia chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16926 Thymbra capitata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18048 Phlomis crinita Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21056 Angelica keiskei Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO21056 Angelica keiskei Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9625 Salvia tomentosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24054 Tournefortia sarmentosa Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21056 Angelica keiskei Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9625 Salvia tomentosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24054 Tournefortia sarmentosa Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9625 Salvia tomentosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21396 Spongia vermicularis Species Spongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9625 Salvia tomentosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19148 Gouania tomentosa Species Gobiesocidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29255 Salvia chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16926 Thymbra capitata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21056 Angelica keiskei Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18048 Phlomis crinita Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24054 Tournefortia sarmentosa Species Heliotropiaceae 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
NPO16926 Thymbra capitata Post-distilled extract n.a. 0.93 ± 0.10 n.a. n.a. mg/g PMID[36557924]
NPO16926 Thymbra capitata Post-distilled extract n.a. 0.93 ± 0.24 n.a. n.a. mg/g PMID[36557924]
NPO18048 Phlomis crinita Methanolic extract Flowers 0.64 ± 0.03 n.a. n.a. % PMID[39419301]
NPO49209 Thymus pulegioides n.a. n.a. 27.61 ± 0.001 n.a. n.a. mg/g PMID[36829949]
NPO53896 Thymus glabrescens n.a. n.a. 24.37 ± 1.848 n.a. n.a. mg/g PMID[36829949]
NPO55161 Thymus alpestris n.a. n.a. 16.25 ± 0.001 n.a. n.a. mg/g PMID[36829949]
NPO59850 Mentha cervina n.a. n.a. 6.0 ± 0.3 n.a. n.a. mg/g PMID[37570937]
NPO61275 Thymus panonicus n.a. n.a. 21.92 ± 0.001 n.a. n.a. mg/g PMID[36829949]
NPO63798 Thymus pulcherimus n.a. n.a. 48.16 ± 0.037 n.a. n.a. mg/g PMID[36829949]
NPO9625 Salvia tomentosa n.a. n.a. 0.00 n.a. n.a. mg/100g PMID[38338335]
NPO9625 Salvia tomentosa n.a. n.a. 34.63 ± 0.49 n.a. n.a. mg/100g PMID[38338335]

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
NPT13 Individual protein Tyrosine-protein kinase LCK Homo sapiens IC50 = 23500.0 nM PMID[19427202]
NPT233 Individual protein Carbonic anhydrase II Homo sapiens Ki = 9594.4 nM PMID[26498393]
NPT1062 Individual protein Carbonic anhydrase IV Homo sapiens Ki = 66.6 nM PMID[26498393]
NPT2719 Individual protein Voltage-gated L-type calcium channel alpha-1C subunit Rattus norvegicus IC50 = 38300.0 nM n.a.
NPT955 Individual protein Carbonic anhydrase VII Homo sapiens Ki = 71.4 nM PMID[26498393]
NPT3825 Individual protein Purinergic receptor P2Y1 Homo sapiens Ki = 20300.0 nM PMID[34731765]
NPT36 Individual protein Tyrosine-protein kinase SRC Homo sapiens IC50 = 36200.0 nM PMID[19427202]
NPT37 Individual protein Signal transducer and activator of transcription 1-alpha/beta Homo sapiens Inhibition = 41.0 % PMID[19427202]
NPT39 Individual protein Signal transducer and activator of transcription 5B Homo sapiens Inhibition = 30.2 % PMID[19427202]
NPT949 Individual protein Carbonic anhydrase XII Homo sapiens Ki = 39.8 nM PMID[26498393]
NPT38 Individual protein Signal transducer and activator of transcription 3 Homo sapiens Inhibition = 32.0 % PMID[19427202]
NPT947 Individual protein Carbonic anhydrase I Homo sapiens Ki > 10000.0 nM PMID[26498393]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT6530 Cell line MOLM-13 Homo sapiens IC50 = 2500.0 nM PMID[30370766]
NPT1649 Cell line MV4-11 Homo sapiens IC50 > 10000.0 nM PMID[30370766]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 590.0 nM PMID[12027757]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 7.3 n.a. PMID[12027757]
NPT24396 Cell line MOLM-14 Homo sapiens IC50 = 6200.0 nM PMID[30370766]
NPT19 Organism Escherichia coli Escherichia coli MIC = 4.0 ug.mL-1 PMID[29477271]
NPT19 Organism Escherichia coli Escherichia coli MIC < 0.125 ug.mL-1 PMID[29477271]
NPT19 Organism Escherichia coli Escherichia coli MIC = 16.0 ug.mL-1 PMID[29477271]

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 NPC38473 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
0.7586 Intermediate Similarity NPC18074
0.7586 Intermediate Similarity NPC5419
0.7586 Intermediate Similarity NPC25581
0.7586 Intermediate Similarity NPC61
0.7049 Intermediate Similarity NPC198388
0.6176 Remote Similarity NPC289690
0.6029 Remote Similarity NPC486819
0.6027 Remote Similarity NPC160378
0.5667 Remote Similarity NPC217052
0.5667 Remote Similarity NPC329344
0.5667 Remote Similarity NPC237506
0.5667 Remote Similarity NPC32626
0.5513 Remote Similarity NPC41494
0.5513 Remote Similarity NPC186100
0.5513 Remote Similarity NPC189197
0.5507 Remote Similarity NPC179505
0.5484 Remote Similarity NPC278652
0.5443 Remote Similarity NPC272750
0.5385 Remote Similarity NPC251407
0.5385 Remote Similarity NPC168653
0.5231 Remote Similarity NPC132921
0.5185 Remote Similarity NPC301089
0.5139 Remote Similarity NPC156709
0.5139 Remote Similarity NPC279676

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC38473 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