Natural Product: NPC217520

Natural Product IDNPC217520
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 [(2R,3S,4S,5R,6S)-6-[5,7-Dihydroxy-2-(4-Hydroxy-3-Methoxyphenyl)-4-Oxochromen-3-Yl]Oxy-3,4,5-Trihydroxyoxan-2-Yl]Methyl (E)-3-(4-Hydroxyphenyl)Prop-2-Enoate
IUPAC Name [(2R,3S,4S,5R,6S)-6-[5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-4-oxochromen-3-yl]oxy-3,4,5-trihydroxyoxan-2-yl]methyl (E)-3-(4-hydroxyphenyl)prop-2-enoate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL233903
PubChem CID 44429737
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0003678] Flavonoid 3-O-p-coumaroyl glycosides

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 TVMGLJJYKIHJNJ-SETHOQODSA-N
Standard InCHI InChI=1S/C31H28O14/c1-41-20-10-15(5-8-18(20)34)29-30(26(38)24-19(35)11-17(33)12-21(24)43-29)45-31-28(40)27(39)25(37)22(44-31)13-42-23(36)9-4-14-2-6-16(32)7-3-14/h2-12,22,25,27-28,31-35,37,39-40H,13H2,1H3/b9-4+/t22-,25-,27+,28-,31+/m1/s1
SMILES COc1cc(ccc1O)c1oc2cc(O)cc(c2c(=O)c1O[C@@H]1O[C@H](COC(=O)/C=C/c2ccc(cc2)O)[C@H]([C@@H]([C@H]1O)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
NPO22304 Morinda morindoides Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[12542353]
NPO28919 Calendula officinalis Species Asteraceae Eukaryota flowers n.a. n.a. PMID[17190444]
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17287127]
NPO2687 Baphia bancoensis Species Fabaceae Eukaryota roots n.a. n.a. PMID[19007285]
NPO22304 Morinda morindoides Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[20149652]
NPO28919 Calendula officinalis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23327299]
NPO28919 Calendula officinalis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[37570937]
NPO22304 Morinda morindoides Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[7775983]
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28919 Calendula officinalis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15308 Stigma croci n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO22304 Morinda morindoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9855 Oricia gabonensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21409 Populus angustifolia Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22434 Cryptosporium pinicola n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO28919 Calendula officinalis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15308 Stigma croci n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO21263 Fructus kochiae n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO15308 Stigma croci n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO21263 Fructus kochiae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO28919 Calendula officinalis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28919 Calendula officinalis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10254 Melaleuca cuticularis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21409 Populus angustifolia Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5429 Vachellia pennatula Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9855 Oricia gabonensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22176 Lasiosiphon kraussianus Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21028 Sasa paniculata Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22304 Morinda morindoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2687 Baphia bancoensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18291 Idea leuconoe Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21276 Sedum forsteri Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22434 Cryptosporium pinicola n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO6536 Marrubium velutinum Species Lamiaceae 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
NPT43 Individual protein Tyrosinase Agaricus bisporus Inhibition = 21.1 % PMID[17287127]

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 NPC217520 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
0.9149 High Similarity NPC139571
0.883 High Similarity NPC477895
0.8791 High Similarity NPC85751
0.8791 High Similarity NPC19240
0.8602 High Similarity NPC223426
0.8152 Intermediate Similarity NPC153755
0.8125 Intermediate Similarity NPC214621
0.8125 Intermediate Similarity NPC34267
0.7938 Intermediate Similarity NPC81042
0.7732 Intermediate Similarity NPC36138
0.7426 Intermediate Similarity NPC470416
0.7273 Intermediate Similarity NPC476472
0.7273 Intermediate Similarity NPC294815
0.7273 Intermediate Similarity NPC16194
0.7216 Intermediate Similarity NPC470125
0.717 Intermediate Similarity NPC474093
0.717 Intermediate Similarity NPC104910
0.71 Intermediate Similarity NPC477629
0.7059 Intermediate Similarity NPC96605
0.7059 Intermediate Similarity NPC280642
0.6979 Remote Similarity NPC609888
0.6972 Remote Similarity NPC488079
0.6961 Remote Similarity NPC218161
0.6915 Remote Similarity NPC223747
0.6875 Remote Similarity NPC25946
0.6842 Remote Similarity NPC203050
0.6842 Remote Similarity NPC225434
0.6771 Remote Similarity NPC116864
0.6771 Remote Similarity NPC244776
0.6768 Remote Similarity NPC129264
0.6667 Remote Similarity NPC21359
0.6667 Remote Similarity NPC460984
0.6569 Remote Similarity NPC104883
0.6569 Remote Similarity NPC488679
0.6372 Remote Similarity NPC488078
0.6316 Remote Similarity NPC241781
0.63 Remote Similarity NPC471079
0.6286 Remote Similarity NPC80068
0.6283 Remote Similarity NPC156785
0.6271 Remote Similarity NPC473554
0.626 Remote Similarity NPC475179
0.625 Remote Similarity NPC270448
0.625 Remote Similarity NPC473327
0.6239 Remote Similarity NPC480796
0.6239 Remote Similarity NPC472993
0.6238 Remote Similarity NPC173582
0.6238 Remote Similarity NPC265885
0.6238 Remote Similarity NPC181465
0.6238 Remote Similarity NPC215710
0.6238 Remote Similarity NPC473438
0.6238 Remote Similarity NPC253788
0.6216 Remote Similarity NPC470718
0.619 Remote Similarity NPC270675
0.619 Remote Similarity NPC195685
0.6182 Remote Similarity NPC470712
0.614 Remote Similarity NPC162394
0.6095 Remote Similarity NPC37668
0.6091 Remote Similarity NPC173837
0.6078 Remote Similarity NPC67326
0.6055 Remote Similarity NPC89052
0.6053 Remote Similarity NPC470713
0.6038 Remote Similarity NPC205824
0.602 Remote Similarity NPC175107
0.6019 Remote Similarity NPC203259
0.6019 Remote Similarity NPC33054
0.6019 Remote Similarity NPC176740
0.6019 Remote Similarity NPC471725
0.6019 Remote Similarity NPC470450
0.6019 Remote Similarity NPC134532
0.6019 Remote Similarity NPC156869
0.6019 Remote Similarity NPC602582
0.6 Remote Similarity NPC474522
0.5963 Remote Similarity NPC478277
0.5963 Remote Similarity NPC478276
0.5963 Remote Similarity NPC478275
0.5963 Remote Similarity NPC92815
0.5909 Remote Similarity NPC121703
0.5872 Remote Similarity NPC472994
0.5859 Remote Similarity NPC219904
0.5854 Remote Similarity NPC487502
0.5833 Remote Similarity NPC111929
0.5833 Remote Similarity NPC320283
0.5833 Remote Similarity NPC471669
0.5833 Remote Similarity NPC41121
0.5818 Remote Similarity NPC483765
0.58 Remote Similarity NPC120099
0.578 Remote Similarity NPC260504
0.578 Remote Similarity NPC89809
0.5773 Remote Similarity NPC77672
0.5773 Remote Similarity NPC133671
0.5773 Remote Similarity NPC135391
0.5773 Remote Similarity NPC78263
0.5773 Remote Similarity NPC250069
0.5766 Remote Similarity NPC599948
0.5758 Remote Similarity NPC325555
0.5758 Remote Similarity NPC226304
0.5755 Remote Similarity NPC296018
0.5748 Remote Similarity NPC487501
0.5741 Remote Similarity NPC101399
0.5741 Remote Similarity NPC221288
0.5741 Remote Similarity NPC217822
0.5741 Remote Similarity NPC11847
0.5741 Remote Similarity NPC198938
0.5741 Remote Similarity NPC194836
0.5741 Remote Similarity NPC91493
0.5741 Remote Similarity NPC605081
0.5727 Remote Similarity NPC483767
0.5727 Remote Similarity NPC483769
0.5727 Remote Similarity NPC483768
0.5727 Remote Similarity NPC483766
0.5676 Remote Similarity NPC603856
0.5644 Remote Similarity NPC101026
0.5644 Remote Similarity NPC488077
0.5631 Remote Similarity NPC4390
0.5619 Remote Similarity NPC39834
0.5612 Remote Similarity NPC127546
0.5612 Remote Similarity NPC57625
0.5612 Remote Similarity NPC173637
0.5612 Remote Similarity NPC317489
0.5612 Remote Similarity NPC223424
0.5612 Remote Similarity NPC600591
0.561 Remote Similarity NPC275977
0.5607 Remote Similarity NPC154741
0.56 Remote Similarity NPC472459
0.5575 Remote Similarity NPC189564
0.5556 Remote Similarity NPC145038
0.5556 Remote Similarity NPC56077
0.5556 Remote Similarity NPC281131
0.5556 Remote Similarity NPC253662
0.5556 Remote Similarity NPC249560
0.5556 Remote Similarity NPC265530
0.5556 Remote Similarity NPC179950
0.5556 Remote Similarity NPC88789
0.5556 Remote Similarity NPC491374
0.5546 Remote Similarity NPC470720
0.5545 Remote Similarity NPC60735
0.5545 Remote Similarity NPC26230
0.5545 Remote Similarity NPC220173
0.5526 Remote Similarity NPC219043
0.5521 Remote Similarity NPC291153
0.5521 Remote Similarity NPC54802
0.5521 Remote Similarity NPC197304
0.552 Remote Similarity NPC72554
0.5514 Remote Similarity NPC473571
0.5514 Remote Similarity NPC110941
0.5505 Remote Similarity NPC476620
0.55 Remote Similarity NPC10205
0.549 Remote Similarity NPC609478
0.5484 Remote Similarity NPC231787
0.5464 Remote Similarity NPC288084
0.5463 Remote Similarity NPC488074
0.5462 Remote Similarity NPC471030
0.5455 Remote Similarity NPC192539
0.5444 Remote Similarity NPC279989
0.5437 Remote Similarity NPC206123
0.5426 Remote Similarity NPC487500
0.5424 Remote Similarity NPC488734
0.5424 Remote Similarity NPC488735
0.5424 Remote Similarity NPC488739
0.5424 Remote Similarity NPC488732
0.5424 Remote Similarity NPC488738
0.5405 Remote Similarity NPC470447
0.54 Remote Similarity NPC64305
0.5397 Remote Similarity NPC30011
0.5392 Remote Similarity NPC159579
0.5391 Remote Similarity NPC292019
0.5391 Remote Similarity NPC202908
0.5378 Remote Similarity NPC480445
0.5357 Remote Similarity NPC470449
0.5349 Remote Similarity NPC97817
0.5345 Remote Similarity NPC164704
0.5333 Remote Similarity NPC488740
0.5333 Remote Similarity NPC488736
0.5333 Remote Similarity NPC488733
0.5333 Remote Similarity NPC470717
0.5321 Remote Similarity NPC488073
0.5321 Remote Similarity NPC126784
0.5321 Remote Similarity NPC241423
0.5306 Remote Similarity NPC276222
0.5306 Remote Similarity NPC274618
0.5306 Remote Similarity NPC118284
0.5306 Remote Similarity NPC608147
0.5263 Remote Similarity NPC470455
0.5254 Remote Similarity NPC470716
0.5253 Remote Similarity NPC67037
0.5253 Remote Similarity NPC255615
0.5246 Remote Similarity NPC488737
0.5238 Remote Similarity NPC488072
0.5221 Remote Similarity NPC470445
0.5214 Remote Similarity NPC470715
0.52 Remote Similarity NPC135599
0.52 Remote Similarity NPC73855
0.52 Remote Similarity NPC113968
0.52 Remote Similarity NPC328940
0.52 Remote Similarity NPC277174
0.52 Remote Similarity NPC606877
0.5192 Remote Similarity NPC197285
0.5192 Remote Similarity NPC601710
0.5179 Remote Similarity NPC486577

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC217520 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
0.6019 Remote Similarity NPD6797 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