Natural Product: NPC207179

Natural Product IDNPC207179
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Ddd01025622
IUPAC Name (2R,3S)-2-(4-hydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3437595
PubChem CID 442154
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0000337] Flavans
          • [CHEMONTID:0003012] Flavan-3-ols

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 RSYUFYQTACJFML-DZGCQCFKSA-N
Standard InCHI InChI=1S/C15H14O5/c16-9-3-1-8(2-4-9)15-13(19)7-11-12(18)5-10(17)6-14(11)20-15/h1-6,13,15-19H,7H2/t13-,15+/m0/s1
SMILES Oc1ccc(cc1)[C@H]1Oc2cc(O)cc(c2C[C@@H]1O)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
NPO30240 Bergenia ligulata Species Saxifragaceae Eukaryota n.a. n.a. n.a. PMID[18622126]
NPO30240 Bergenia ligulata Species Saxifragaceae Eukaryota volatile oil n.a. n.a. PMID[21639116]
NPO41406 Escherichia coli + Escherichia coli coculture Species n.a. n.a. n.a. n.a. n.a. PMID[26860871]
NPO17083 Atraphaxis frutescens Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[28006914]
NPO41560 Three-strain Escherichia coli polyculture Strain n.a. n.a. n.a. n.a. n.a. PMID[28588129]
NPO41406 Escherichia coli + Escherichia coli coculture Species n.a. n.a. n.a. n.a. n.a. PMID[29318204]
NPO41406 Escherichia coli + Escherichia coli coculture Species n.a. n.a. n.a. n.a. n.a. PMID[29362971]
NPO41406 Escherichia coli + Escherichia coli coculture Species n.a. n.a. n.a. n.a. n.a. PMID[31125607]
NPO41406 Escherichia coli + Escherichia coli coculture Species n.a. n.a. n.a. n.a. n.a. PMID[32285175]
NPO41406 Escherichia coli + Escherichia coli coculture Species n.a. n.a. n.a. n.a. n.a. PMID[33930665]
NPO1334 Senegalia catechu Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17083 Atraphaxis frutescens Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29757 Acacia catechu Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30240 Bergenia ligulata Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29757 Acacia catechu Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8635 Sapindus delavayi Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1334 Senegalia catechu Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29757 Acacia catechu Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1334 Senegalia catechu Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17083 Atraphaxis frutescens Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6010 Haeckeria punctulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28393 Urospora penicilliformis Species Ulotrichaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1334 Senegalia catechu Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23956 Trichoderma deliquescens Species Hypocreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8635 Sapindus delavayi Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11526 Vismia latifolia Species Hypericaceae 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
NPT21965 Single protein Tryptophan--tRNA ligase Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) Percent Effect = 4.292 % DOI[10.6019/CHEMBL3988442]
NPT21964 Single protein Histidine--tRNA ligase Trypanosoma cruzi (strain CL Brener) Percent Effect = 3.96 % DOI[10.6019/CHEMBL3988442]
NPT21962 Single protein Methionyl-tRNA synthetase, putative Leishmania donovani (strain BPK282A1) Inhibition = 12.09 % DOI[10.6019/CHEMBL3988442]
NPT21968 Single protein Histidine--tRNA ligase Leishmania infantum Percent Effect = 19.44 % DOI[10.6019/CHEMBL3988442]
NPT21966 Single protein Polyketide synthase Pks13 Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) Percent Effect = -28.12 % DOI[10.6019/CHEMBL3988442]
NPT3565 Individual protein Lysine--tRNA ligase Plasmodium falciparum (isolate 3D7) Percent Effect = 6.69 % DOI[10.6019/CHEMBL3988442]
NPT21963 Single protein Coenzyme A biosynthesis bifunctional protein CoaBC Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) Percent Effect = 12.87 % DOI[10.6019/CHEMBL3988442]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT65 Cell line HepG2 Homo sapiens INHIBITION = 4.94 % PMID[32078764]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum INHIBITION = 1.11 % PMID[32078764]
NPT21970 Organism Wolbachia pipientis Wolbachia pipientis Percent Effect = 2.317 % DOI[10.6019/CHEMBL3988442]
NPT844 Organism Trypanosoma brucei rhodesiense Trypanosoma brucei rhodesiense Activity = 96.07 % PMID[34965114]
NPT844 Organism Trypanosoma brucei rhodesiense Trypanosoma brucei rhodesiense IC50 = 28.28 ug.mL-1 PMID[34965114]
NPT844 Organism Trypanosoma brucei rhodesiense Trypanosoma brucei rhodesiense IC50 = 4.03 ug.mL-1 PMID[34965114]
NPT844 Organism Trypanosoma brucei rhodesiense Trypanosoma brucei rhodesiense Activity = 99.71 % PMID[34965114]
NPT2229 Organism Trypanosoma brucei gambiense Trypanosoma brucei gambiense IC50 = 46.37 ug.mL-1 PMID[34965114]
NPT843 Organism Trypanosoma evansi Trypanosoma evansi IC50 = 14.44 ug.mL-1 PMID[34965114]
NPT2229 Organism Trypanosoma brucei gambiense Trypanosoma brucei gambiense Activity = 90.28 % PMID[34965114]
NPT844 Organism Trypanosoma brucei rhodesiense Trypanosoma brucei rhodesiense IC50 = 45.73 ug.mL-1 PMID[34965114]
NPT843 Organism Trypanosoma evansi Trypanosoma evansi Activity = 99.7 % PMID[34965114]
NPT844 Organism Trypanosoma brucei rhodesiense Trypanosoma brucei rhodesiense Activity = 99.57 % PMID[34965114]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi Percent Effect = -121.46 % DOI[10.6019/CHEMBL3988442]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis Percent Effect = -4.634 % DOI[10.6019/CHEMBL3988442]
NPT21967 Protein complex ClpP1P2 Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) Percent Effect = -12.57 % DOI[10.6019/CHEMBL3988442]
NPT633 Organism Leishmania donovani Leishmania donovani Percent Effect = 20.66 % DOI[10.6019/CHEMBL3988442]
NPT474 Organism Plasmodium berghei Plasmodium berghei INHIBITION = 12.28 % PMID[32078764]
NPT474 Organism Plasmodium berghei Plasmodium berghei INHIBITION = 7.5 % PMID[32078764]
NPT1018 Organism Trypanosoma brucei Trypanosoma brucei Percent Effect = -6.928 % DOI[10.6019/CHEMBL3988442]
NPT2 Others Unspecified n.a. Inhibition = -11.95 % DOI[10.6019/CHEMBL3507680]
NPT471 Organism Trypanosoma brucei brucei Trypanosoma brucei brucei IC50 = 38.63 ug.mL-1 PMID[34965114]
NPT471 Organism Trypanosoma brucei brucei Trypanosoma brucei brucei Activity = 98.54 % PMID[34965114]

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 NPC207179 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 NPC167571
1.0 High Similarity NPC278552
0.8222 Intermediate Similarity NPC261619
0.8222 Intermediate Similarity NPC61477
0.8222 Intermediate Similarity NPC78770
0.8222 Intermediate Similarity NPC219876
0.8222 Intermediate Similarity NPC126029
0.8222 Intermediate Similarity NPC15658
0.74 Intermediate Similarity NPC16435
0.74 Intermediate Similarity NPC171932
0.7391 Intermediate Similarity NPC268266
0.7391 Intermediate Similarity NPC42760
0.7391 Intermediate Similarity NPC220825
0.7391 Intermediate Similarity NPC268342
0.7083 Intermediate Similarity NPC47398
0.7083 Intermediate Similarity NPC234333
0.7083 Intermediate Similarity NPC260898
0.7 Intermediate Similarity NPC61946
0.6458 Remote Similarity NPC482472
0.6379 Remote Similarity NPC277331
0.6379 Remote Similarity NPC100482
0.6102 Remote Similarity NPC601999
0.6078 Remote Similarity NPC62290
0.6078 Remote Similarity NPC142731
0.6078 Remote Similarity NPC326506
0.6066 Remote Similarity NPC308402
0.6066 Remote Similarity NPC28440
0.6032 Remote Similarity NPC211561
0.5833 Remote Similarity NPC58190
0.5833 Remote Similarity NPC108811
0.5833 Remote Similarity NPC9636
0.5833 Remote Similarity NPC170103
0.5833 Remote Similarity NPC236202
0.5833 Remote Similarity NPC262911
0.5833 Remote Similarity NPC202742
0.58 Remote Similarity NPC601844
0.5738 Remote Similarity NPC246202
0.5738 Remote Similarity NPC224161
0.5738 Remote Similarity NPC46335
0.5738 Remote Similarity NPC294558
0.5738 Remote Similarity NPC18185
0.5738 Remote Similarity NPC263940
0.5738 Remote Similarity NPC279406
0.5738 Remote Similarity NPC486519
0.5714 Remote Similarity NPC155564
0.5625 Remote Similarity NPC70409
0.5625 Remote Similarity NPC204770
0.5625 Remote Similarity NPC600551
0.5625 Remote Similarity NPC601980
0.5625 Remote Similarity NPC602065
0.5625 Remote Similarity NPC611024
0.5574 Remote Similarity NPC607430
0.5538 Remote Similarity NPC601997
0.5538 Remote Similarity NPC609211
0.5538 Remote Similarity NPC610665
0.5455 Remote Similarity NPC186228
0.5373 Remote Similarity NPC134911
0.5323 Remote Similarity NPC82917
0.5312 Remote Similarity NPC313116
0.5312 Remote Similarity NPC603340
0.5303 Remote Similarity NPC226809
0.5246 Remote Similarity NPC96576
0.5192 Remote Similarity NPC1940
0.5179 Remote Similarity NPC36835
0.5179 Remote Similarity NPC246162
0.5179 Remote Similarity NPC9743
0.5179 Remote Similarity NPC260491
0.5179 Remote Similarity NPC61506
0.5179 Remote Similarity NPC240476
0.5152 Remote Similarity NPC470802
0.5147 Remote Similarity NPC46283
0.5147 Remote Similarity NPC469944
0.5147 Remote Similarity NPC278548
0.5143 Remote Similarity NPC306267
0.5091 Remote Similarity NPC103799
0.5085 Remote Similarity NPC150670
0.5085 Remote Similarity NPC482704
0.5082 Remote Similarity NPC156818

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC207179 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
0.8222 Intermediate Similarity NPD1612 Clinical (unspecified phase)
0.8222 Intermediate Similarity NPD1613 Phase 4

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