Natural Product: NPC191146

Natural Product IDNPC191146
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Gartanin
IUPAC Name 1,3,5,8-tetrahydroxy-2,4-bis(3-methylbut-2-enyl)xanthen-9-one
Synonyms Gartanin
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL487992
PubChem CID 5281633
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0002817] Dibenzopyrans
            • [CHEMONTID:0000200] Xanthenes
              • [CHEMONTID:0000204] Xanthones
                • [CHEMONTID:0003518] 4-prenylated xanthones

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 OJXQLGQIDIPMTE-UHFFFAOYSA-N
Standard InCHI InChI=1S/C23H24O6/c1-11(2)5-7-13-19(26)14(8-6-12(3)4)22-18(20(13)27)21(28)17-15(24)9-10-16(25)23(17)29-22/h5-6,9-10,24-27H,7-8H2,1-4H3
SMILES CC(=CCc1c(c(CC=C(C)C)c2c(c1O)c(=O)c1c(ccc(c1o2)O)O)O)C

  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
NPO3806 Garcinia morella Species Clusiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0040-4039(00)90246-6]
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[10075773]
NPO27239 Maclura tinctoria Species Moraceae Eukaryota n.a. n.a. n.a. PMID[11087602]
NPO27239 Maclura tinctoria Species Moraceae Eukaryota n.a. stem n.a. PMID[12932124]
NPO27239 Maclura tinctoria Species Moraceae Eukaryota n.a. n.a. n.a. PMID[12932124]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. PMID[16933891]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[18464091]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[18558747]
NPO7920 Pentadesma butyracea Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[19296616]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO6871 Garcinia staudtii Species Clusiaceae Eukaryota twigs n.a. n.a. PMID[19604701]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota stem bark Pangradin village, Jasinga, West Java, Indonesia 2005-AUG PMID[19839614]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[20817450]
NPO32914 Garcinia propinqua Species Clusiaceae Eukaryota twigs n.a. n.a. PMID[22963193]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. pericarp n.a. PMID[24555285]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[24717154]
NPO32914 Garcinia propinqua Species Clusiaceae Eukaryota Stem Bark n.a. n.a. PMID[28489373]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota fruit hulls Madras, Tamil Nadu, India 1993-MAR PMID[9213587]
NPO9741 Actinopyga agassizi Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3707 Chromatium okenii Species Chromatiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO7920 Pentadesma butyracea Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3806 Garcinia morella Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22337 Garcinia dulcis Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9717 Wibelia divaricata Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12600 Trametes cinnabarina Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10221 Streptomyces alboniger Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO27924 Serpocaulon triseriale Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25216 Senecio vellereus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8927 Poria selecta Species Coccinellidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27239 Maclura tinctoria Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10056 Nicotiana sylvestris Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24931 Myelochroa aurulenta Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3449 Lonicera hypoleuca Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7534 Leptogorgia sarmentosa Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4064 Halimodendron halodendron Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8354 Aster bellidiastrum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8560 Aplidium tabascum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3806 Garcinia morella Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22337 Garcinia dulcis Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22337 Garcinia dulcis Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3806 Garcinia morella Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3806 Garcinia morella Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10221 Streptomyces alboniger Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO8560 Aplidium tabascum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9741 Actinopyga agassizi Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3707 Chromatium okenii Species Chromatiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6249 Garcinia mangostana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27924 Serpocaulon triseriale Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10391 Dolomiaea souliei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4064 Halimodendron halodendron Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10376 Arcyria denudata Species Trichiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8354 Aster bellidiastrum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12600 Trametes cinnabarina Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3449 Lonicera hypoleuca Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3806 Garcinia morella Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6871 Garcinia staudtii Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10056 Nicotiana sylvestris Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7534 Leptogorgia sarmentosa Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24931 Myelochroa aurulenta Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10849 Eucalyptus camaldulensis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8927 Poria selecta Species Coccinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9717 Wibelia divaricata Species Davalliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27239 Maclura tinctoria Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7811 Scleronephthya pallida Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7920 Pentadesma butyracea Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25216 Senecio vellereus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22337 Garcinia dulcis Species Clusiaceae 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
NPT163 Individual protein Nuclear factor NF-kappa-B p105 subunit Homo sapiens IC50 > 20000.0 nM PMID[19839614]
NPT344 Individual protein Sialidase Clostridium perfringens IC50 = 2900.0 nM PMID[20696581]
NPT344 Individual protein Sialidase Clostridium perfringens Ki = 3600.0 nM PMID[20696581]
NPT344 Individual protein Sialidase Clostridium perfringens Ki = 436.66 nM PMID[20696581]
NPT3892 Individual protein Tumor necrosis factor receptor superfamily member 10B Homo sapiens FC = 3.1 n.a. PMID[19788289]
NPT861 Individual protein Isocitrate dehydrogenase [NADP] cytoplasmic Homo sapiens Activity = 93.9 % PMID[26508549]
NPT861 Individual protein Isocitrate dehydrogenase [NADP] cytoplasmic Homo sapiens Activity = 89.9 % PMID[26508549]
NPT441 Individual protein Cytochrome P450 19A1 Homo sapiens Activity = 75.9 % PMID[18558747]
NPT721 Individual protein Nuclear factor NF-kappa-B p65 subunit Homo sapiens IC50 = 19000.0 nM PMID[19839614]
NPT29659 Single protein NEDD8-conjugating enzyme Ubc12 Homo sapiens IC50 = 10330.0 nM PMID[35131538]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT315 Cell line CEM-SS Homo sapiens IC50 = 5.3 ug.mL-1 PMID[11087602]
NPT83 Cell line MCF7 Homo sapiens IC50 = 1.2 ug.mL-1 PMID[19296616]
NPT139 Cell line HT-29 Homo sapiens ED50 > 10.0 uM PMID[19839614]
NPT181 Cell line Bel-7402 Homo sapiens IC50 = 7780.0 nM PMID[30684866]
NPT1225 Organism Plasmodium falciparum (isolate FcB1 / Columbia) Plasmodium falciparum FcB1/Columbia IC50 = 3.1 ug.mL-1 PMID[19296616]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium MIC = 128.0 ug.mL-1 PMID[22963193]
NPT2647 Organism Drechslera Drechslera Inhibition = 18.0 % PMID[9213587]
NPT2647 Organism Drechslera Drechslera Inhibition = 54.0 % PMID[9213587]
NPT2647 Organism Drechslera Drechslera Inhibition = 75.0 % PMID[9213587]
NPT2647 Organism Drechslera Drechslera Inhibition = 71.0 % PMID[9213587]
NPT2648 Organism Fusarium oxysporum f. sp. vasinfectum Fusarium oxysporum f. sp. vasinfectum Inhibition = 3.0 % PMID[9213587]
NPT2648 Organism Fusarium oxysporum f. sp. vasinfectum Fusarium oxysporum f. sp. vasinfectum Inhibition = 4.0 % PMID[9213587]
NPT2648 Organism Fusarium oxysporum f. sp. vasinfectum Fusarium oxysporum f. sp. vasinfectum Inhibition = 9.0 % PMID[9213587]
NPT2648 Organism Fusarium oxysporum f. sp. vasinfectum Fusarium oxysporum f. sp. vasinfectum Inhibition = 12.0 % PMID[9213587]
NPT2646 Organism Alternaria tenuis Alternaria tenuis Inhibition = 4.0 % PMID[9213587]
NPT2646 Organism Alternaria tenuis Alternaria tenuis Inhibition = 20.0 % PMID[9213587]
NPT2646 Organism Alternaria tenuis Alternaria tenuis Inhibition = 22.0 % PMID[9213587]
NPT2646 Organism Alternaria tenuis Alternaria tenuis Inhibition = 29.0 % PMID[9213587]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 32.0 ug.mL-1 PMID[19604701]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 128.0 ug.mL-1 PMID[22963193]
NPT19 Organism Escherichia coli Escherichia coli MIC = 128.0 ug.mL-1 PMID[22963193]
NPT2 Others Unspecified n.a. Ratio IC50 = 0.39 n.a. PMID[19296616]

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 NPC191146 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 NPC33051
0.6833 Remote Similarity NPC138243
0.625 Remote Similarity NPC78225
0.619 Remote Similarity NPC37135
0.619 Remote Similarity NPC69769
0.5735 Remote Similarity NPC68093
0.5634 Remote Similarity NPC204290
0.5556 Remote Similarity NPC223988
0.5538 Remote Similarity NPC70433
0.5479 Remote Similarity NPC483041
0.5373 Remote Similarity NPC599982
0.5224 Remote Similarity NPC190637
0.5224 Remote Similarity NPC482709
0.5217 Remote Similarity NPC304008
0.5147 Remote Similarity NPC204985
0.5147 Remote Similarity NPC122146
0.5143 Remote Similarity NPC187745
0.5072 Remote Similarity NPC171916

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC191146 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