Natural Product: NPC210192

Natural Product IDNPC210192
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Stilbostemin H 3'-Beta-D-Glucopyranoside
IUPAC Name (2S,3R,4S,5S,6R)-2-[3-hydroxy-5-[2-(4-methoxyphenyl)ethyl]-2-methylphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL495844
PubChem CID 11625932
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 IELQQKDOYFODON-QMCAAQAGSA-N
Standard InCHI InChI=1S/C22H28O8/c1-12-16(24)9-14(4-3-13-5-7-15(28-2)8-6-13)10-17(12)29-22-21(27)20(26)19(25)18(11-23)30-22/h5-10,18-27H,3-4,11H2,1-2H3/t18-,19-,20+,21-,22-/m1/s1
SMILES OC[C@H]1O[C@@H](Oc2cc(CCc3ccc(cc3)OC)cc(c2C)O)[C@@H]([C@H]([C@@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   420.18 Volume:   417.902
?
Van der Waals volume.
Dense:   1.005 LogP:   2.088
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.282
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.207
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   18.0
TPSA:   128.84
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   5.0 Rings:   3.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.442 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.586 Fsp3:   0.455
MCE-18:   66.25
?
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:   0 PAINS Alert:   0
Colloidal aggregators:   0.518 Fluc inhibitor:   0.252
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.151
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.295
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.097 Promiscuous compounds:   0.105

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.634 MDCK Permeability:   -4.888
Pgp-inhibitor:   0.02 Pgp-substrate:   0.125
PAMPA:   0.73
?
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):   0.908
20% Bioavailability (F20%):   0.605 30% Bioavailability (F30%):   0.976
50% Bioavailability (F50%):   0.96

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.055 MRP1:   0.122
Plasma Protein Binding (PPB):   85.262% Volume Distribution (VD):   -0.019
Fu: 15.608%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.128
BSEP inhibitor:   0.316

ADMET: Metabolism

CYP1A2-inhibitor:   0.971 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.997 CYP2C19-substrate:   0.754
CYP2C9-inhibitor:   0.773 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.063
CYP3A4-inhibitor:   0.579 CYP3A4-substrate:   0.072
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.566
?
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):  4.876 Half-life (T1/2):  2.959

ADMET: Toxicity

hERG Blockers:  0.179 hERG Blockers (10um):  0.39
Human Hepatotoxicity (H-HT):  0.742 Drug-induced Liver Injury (DILI):  0.664
AMES Toxicity:  0.885 Rat Oral Acute Toxicity:  0.012
Maximum Recommended Daily Dose:  0.04 Skin Sensitization:  0.994
Carcinogencity:  0.108 Eye Corrosion:  0.0
Eye Irritation:  0.199 Respiratory Toxicity:  0.039
Drug-induced Neurotoxicity:  0.022 Ototoxicity:  0.96
Hematotoxicity:  0.41 Drug-induced Nephrotoxicity:  0.883
Genotoxicity:  0.061 RPMI-8226 Immunitoxicity:  0.142
A549 Cytotoxicity:  0.578 Hek293 Cytotoxicity:  0.489
BCF:   0.851
?
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:   3.48
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.088
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.284
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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
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. n.a. n.a. PMID[15679323]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota roots n.a. n.a. PMID[16643052]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota Roots; Stems; Tubers n.a. n.a. PMID[16872143]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota roots n.a. n.a. PMID[18452334]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. rhizome n.a. PMID[21902195]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. tuberous root n.a. PMID[21902195]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19620 Stemona tuberosa Species Stemonaceae 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
NPT519 Cell line SH-SY5Y Homo sapiens Activity = 31.0 % PMID[23634786]
NPT519 Cell line SH-SY5Y Homo sapiens Activity = 65.6 % PubChem BioAssay data set

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 NPC210192 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
0.8167 Intermediate Similarity NPC134260
0.6232 Remote Similarity NPC189115
0.6167 Remote Similarity NPC60589
0.6167 Remote Similarity NPC469708
0.6094 Remote Similarity NPC270849
0.6027 Remote Similarity NPC61594
0.5946 Remote Similarity NPC56735
0.5846 Remote Similarity NPC472024
0.5616 Remote Similarity NPC30432
0.5606 Remote Similarity NPC19470
0.5571 Remote Similarity NPC294166
0.5571 Remote Similarity NPC115022
0.5556 Remote Similarity NPC475096
0.5538 Remote Similarity NPC9912
0.5526 Remote Similarity NPC147596
0.5522 Remote Similarity NPC26653
0.5522 Remote Similarity NPC80600
0.5479 Remote Similarity NPC177742
0.5469 Remote Similarity NPC69513
0.5455 Remote Similarity NPC218685
0.5417 Remote Similarity NPC604892
0.5405 Remote Similarity NPC605700
0.5373 Remote Similarity NPC479028
0.5373 Remote Similarity NPC23084
0.5373 Remote Similarity NPC479031
0.5362 Remote Similarity NPC599943
0.5312 Remote Similarity NPC12308
0.5303 Remote Similarity NPC215833
0.5294 Remote Similarity NPC210015
0.5263 Remote Similarity NPC76128
0.5246 Remote Similarity NPC212729
0.5246 Remote Similarity NPC604498
0.5238 Remote Similarity NPC152722
0.52 Remote Similarity NPC146837
0.52 Remote Similarity NPC606849
0.519 Remote Similarity NPC300537
0.5161 Remote Similarity NPC217854
0.5161 Remote Similarity NPC269242
0.5156 Remote Similarity NPC299144
0.5156 Remote Similarity NPC609376
0.5152 Remote Similarity NPC166040
0.5143 Remote Similarity NPC222455
0.5139 Remote Similarity NPC469661
0.5132 Remote Similarity NPC604833
0.5128 Remote Similarity NPC227902
0.5128 Remote Similarity NPC106625
0.5125 Remote Similarity NPC476203
0.5079 Remote Similarity NPC192810
0.5079 Remote Similarity NPC294470
0.5077 Remote Similarity NPC608788
0.5075 Remote Similarity NPC40377
0.5075 Remote Similarity NPC310661
0.5072 Remote Similarity NPC26080
0.5072 Remote Similarity NPC165686
0.5068 Remote Similarity NPC479030
0.5068 Remote Similarity NPC111536
0.5068 Remote Similarity NPC8497
0.5068 Remote Similarity NPC604095
0.5067 Remote Similarity NPC99233

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC210192 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