Natural Product: NPC212770

Natural Product IDNPC212770
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (2S,3R,4S,5S,6R)-2-[3-Hydroxy-5-[(E)-2-(4-Hydroxy-3-Methoxyphenyl)Ethenyl]Phenoxy]-6-(Hydroxymethyl)Oxane-3,4,5-Triol
IUPAC Name (2S,3R,4S,5S,6R)-2-[3-hydroxy-5-[(E)-2-(4-hydroxy-3-methoxyphenyl)ethenyl]phenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL113339
PubChem CID 5281716
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000253] Stilbenes
        • [CHEMONTID:0000142] Stilbene 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 KLPUXMNQDCUPNO-DXKBKAGUSA-N
Standard InCHI InChI=1S/C21H24O9/c1-28-16-8-11(4-5-15(16)24)2-3-12-6-13(23)9-14(7-12)29-21-20(27)19(26)18(25)17(10-22)30-21/h2-9,17-27H,10H2,1H3/b3-2+/t17-,18-,19+,20-,21-/m1/s1
SMILES COc1cc(/C=C/c2cc(cc(c2)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)O)ccc1O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   420.14 Volume:   406.76
?
Van der Waals volume.
Dense:   1.033 LogP:   1.718
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.961
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.437
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   19.0
TPSA:   149.07
?
Topological Polar Surface Area.
 H-Bond Acceptor:   9.0
H-Bond Donor:   6.0 Rings:   3.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.366 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.744 Fsp3:   0.333
MCE-18:   67.143
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.614 Fluc inhibitor:   0.994
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.149
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.775
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.286 Promiscuous compounds:   0.242

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.051 MDCK Permeability:   -5.276
Pgp-inhibitor:   0.0 Pgp-substrate:   0.019
PAMPA:   0.85
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.086
20% Bioavailability (F20%):   0.645 30% Bioavailability (F30%):   0.982
50% Bioavailability (F50%):   0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.071
Plasma Protein Binding (PPB):   80.899% Volume Distribution (VD):   -0.236
Fu: 20.172%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.433
BSEP inhibitor:   0.007

ADMET: Metabolism

CYP1A2-inhibitor:   0.006 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.008 CYP2D6-substrate:   0.001
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.005
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.957
HLM stability:   0.125
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  3.521 Half-life (T1/2):  3.89

ADMET: Toxicity

hERG Blockers:  0.066 hERG Blockers (10um):  0.187
Human Hepatotoxicity (H-HT):  0.818 Drug-induced Liver Injury (DILI):  0.726
AMES Toxicity:  0.926 Rat Oral Acute Toxicity:  0.031
Maximum Recommended Daily Dose:  0.107 Skin Sensitization:  0.995
Carcinogencity:  0.229 Eye Corrosion:  0.0
Eye Irritation:  0.424 Respiratory Toxicity:  0.032
Drug-induced Neurotoxicity:  0.019 Ototoxicity:  0.896
Hematotoxicity:  0.166 Drug-induced Nephrotoxicity:  0.712
Genotoxicity:  0.642 RPMI-8226 Immunitoxicity:  0.149
A549 Cytotoxicity:  0.573 Hek293 Cytotoxicity:  0.526
BCF:   0.515
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   3.041
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.629
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.648
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO23656 Typha latifolia Species Typhaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/np50070a031]
NPO88 Rheum undulatum Species Polygonaceae Eukaryota rhizome n.a. n.a. PMID[10714491]
NPO2421 Picea glauca Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[18636777]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[29244495]
NPO284 Albizia procera Species Fabaceae Eukaryota Bark n.a. n.a. PMID[30520635]
NPO1539 Artemisia giraldii Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[36364129]
NPO16773 Picea abies Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[38731619]
NPO3255 Lampranthus sociorum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1539 Artemisia giraldii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO284 Albizia procera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2421 Picea glauca Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3415 Perymenium mendezii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16773 Picea abies Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3963 Hortonia floribunda Species Monimiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5981 Achlys triphylla Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4421 Penicillium cyclopium Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO88 Rheum undulatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23656 Typha latifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19432 Millettia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23656 Typha latifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO99 Artemisia porrecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16773 Picea abies Species Pinaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23656 Typha latifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16773 Picea abies Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19432 Millettia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO99 Artemisia porrecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23656 Typha latifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO88 Rheum undulatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7464 Uruparia lanosa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO4421 Penicillium cyclopium Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5981 Achlys triphylla Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3963 Hortonia floribunda Species Monimiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23656 Typha latifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO284 Albizia procera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4952 Pertusaria amara Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3415 Perymenium mendezii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19432 Millettia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7616 Melanargia galathea Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3263 Thea sasanqua n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO99 Artemisia porrecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16773 Picea abies Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO88 Rheum undulatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2421 Picea glauca Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6844 Bulbophyllum protractum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3255 Lampranthus sociorum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2963 Diospyros glaucifolia Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4117 Nauclea rhynchophylla Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15597 Calystegia pubescens Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29287 Alectoria ochroleuca Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO855 Elymnias thryallis Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1539 Artemisia giraldii Species Asteraceae 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

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
NPT32 Organism Mus musculus Mus musculus IC50 > 100000.0 nM PMID[10714491]
NPT32 Organism Mus musculus Mus musculus Inhibition = 5.0 % PMID[10714491]





 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 NPC212770 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
0.8136 Intermediate Similarity NPC85799
0.8136 Intermediate Similarity NPC303422
0.8065 Intermediate Similarity NPC98777
0.7869 Intermediate Similarity NPC242028
0.7869 Intermediate Similarity NPC294166
0.7869 Intermediate Similarity NPC203230
0.7869 Intermediate Similarity NPC115022
0.7581 Intermediate Similarity NPC65530
0.7541 Intermediate Similarity NPC218003
0.7188 Intermediate Similarity NPC8497
0.6667 Remote Similarity NPC185778
0.6508 Remote Similarity NPC214910
0.6333 Remote Similarity NPC12308
0.6232 Remote Similarity NPC189115
0.6176 Remote Similarity NPC604095
0.6 Remote Similarity NPC26080
0.6 Remote Similarity NPC165686
0.597 Remote Similarity NPC59324
0.5867 Remote Similarity NPC188555
0.5857 Remote Similarity NPC260681
0.5846 Remote Similarity NPC479028
0.5846 Remote Similarity NPC479031
0.5797 Remote Similarity NPC252169
0.5758 Remote Similarity NPC210015
0.5714 Remote Similarity NPC221090
0.5658 Remote Similarity NPC138350
0.5658 Remote Similarity NPC165482
0.5652 Remote Similarity NPC307110
0.5652 Remote Similarity NPC157554
0.5606 Remote Similarity NPC205054
0.56 Remote Similarity NPC130496
0.5571 Remote Similarity NPC469661
0.557 Remote Similarity NPC199928
0.5526 Remote Similarity NPC40664
0.5526 Remote Similarity NPC197723
0.5522 Remote Similarity NPC65942
0.5522 Remote Similarity NPC248307
0.5467 Remote Similarity NPC191046
0.5441 Remote Similarity NPC479029
0.5432 Remote Similarity NPC33298
0.5349 Remote Similarity NPC478885
0.5342 Remote Similarity NPC475084
0.5333 Remote Similarity NPC186406
0.5323 Remote Similarity NPC192810
0.5316 Remote Similarity NPC289346
0.5294 Remote Similarity NPC481303
0.5286 Remote Similarity NPC473045
0.5246 Remote Similarity NPC142319
0.5238 Remote Similarity NPC152722
0.5231 Remote Similarity NPC145900
0.5211 Remote Similarity NPC100389
0.5195 Remote Similarity NPC51328
0.5195 Remote Similarity NPC55158
0.5195 Remote Similarity NPC488085
0.5172 Remote Similarity NPC59692
0.5128 Remote Similarity NPC38041
0.5128 Remote Similarity NPC18979
0.5128 Remote Similarity NPC22150
0.5122 Remote Similarity NPC285108
0.5068 Remote Similarity NPC479030
0.5068 Remote Similarity NPC186418
0.5067 Remote Similarity NPC57587
0.5062 Remote Similarity NPC236934
0.5059 Remote Similarity NPC476865

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC212770 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