Natural Product: NPC59717

Natural Product IDNPC59717
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 KOMUHHCFAXYRPO-NOYZTADKSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44258154
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001737] Flavonoid C-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 KOMUHHCFAXYRPO-NOYZTADKSA-N
Standard InCHI InChI=1S/C22H22O11/c1-31-13-4-8(2-3-9(13)24)12-5-10(25)16-14(32-12)6-11(26)17(19(16)28)22-21(30)20(29)18(27)15(7-23)33-22/h2-6,15,18,20-24,26-30H,7H2,1H3/t15?,18-,20+,21?,22+/m1/s1
SMILES COc1cc(ccc1O)c1cc(=O)c2c(cc(c(c2O)[C@H]2C([C@H]([C@@H](C(CO)O2)O)O)O)O)o1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   462.12 Volume:   430.443
?
Van der Waals volume.
Dense:   1.074 LogP:   0.36
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.197
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.296
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   24.0
TPSA:   190.28
?
Topological Polar Surface Area.
 H-Bond Acceptor:   11.0
H-Bond Donor:   7.0 Rings:   4.0
Heavy Atoms:   11.0

MedChem Properties

QED Drug-Likeness Score:   0.278 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.003 Fsp3:   0.318
MCE-18:   90.31
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.579 Fluc inhibitor:   0.077
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.928
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.897
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.092 Promiscuous compounds:   0.471

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.059 MDCK Permeability:   -5.226
Pgp-inhibitor:   0.0 Pgp-substrate:   0.793
PAMPA:   0.996
?
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):   0.732
20% Bioavailability (F20%):   0.785 30% Bioavailability (F30%):   0.989
50% Bioavailability (F50%):   0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.938
Plasma Protein Binding (PPB):   85.873% Volume Distribution (VD):   0.002
Fu: 12.83%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.384
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.449
BSEP inhibitor:   0.21

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.983 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.37 CYP2D6-substrate:   0.738
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.055
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.999
HLM stability:   0.054
?
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):  3.71 Half-life (T1/2):  3.364

ADMET: Toxicity

hERG Blockers:  0.025 hERG Blockers (10um):  0.217
Human Hepatotoxicity (H-HT):  0.482 Drug-induced Liver Injury (DILI):  0.713
AMES Toxicity:  0.649 Rat Oral Acute Toxicity:  0.218
Maximum Recommended Daily Dose:  0.359 Skin Sensitization:  0.89
Carcinogencity:  0.247 Eye Corrosion:  0.0
Eye Irritation:  0.791 Respiratory Toxicity:  0.199
Drug-induced Neurotoxicity:  0.005 Ototoxicity:  0.617
Hematotoxicity:  0.069 Drug-induced Nephrotoxicity:  0.099
Genotoxicity:  0.86 RPMI-8226 Immunitoxicity:  0.135
A549 Cytotoxicity:  0.359 Hek293 Cytotoxicity:  0.47
BCF:   0.343
?
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:   2.781
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.274
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.424
?
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
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[16562834]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. fruit n.a. PMID[24155209]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[24959987]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[25302569]
NPO9427 Lemna minor Species Araceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7647 Potamogeton natans Species Potamogetonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7647 Potamogeton natans Species Potamogetonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9427 Lemna minor Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9427 Lemna minor Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7647 Potamogeton natans Species Potamogetonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9427 Lemna minor Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7647 Potamogeton natans Species Potamogetonaceae 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





 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 NPC59717 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 NPC111249
0.7838 Intermediate Similarity NPC328740
0.7838 Intermediate Similarity NPC289774
0.7733 Intermediate Similarity NPC53545
0.6744 Remote Similarity NPC603300
0.6585 Remote Similarity NPC10807
0.6585 Remote Similarity NPC161881
0.6375 Remote Similarity NPC289771
0.6375 Remote Similarity NPC268193
0.6292 Remote Similarity NPC47923
0.6222 Remote Similarity NPC218488
0.619 Remote Similarity NPC602537
0.6053 Remote Similarity NPC10097
0.5833 Remote Similarity NPC112701
0.5732 Remote Similarity NPC602497
0.5625 Remote Similarity NPC139966
0.5556 Remote Similarity NPC311830
0.5556 Remote Similarity NPC602805
0.5526 Remote Similarity NPC83508
0.5474 Remote Similarity NPC606373
0.5455 Remote Similarity NPC304745
0.5444 Remote Similarity NPC601710
0.5426 Remote Similarity NPC78734
0.5426 Remote Similarity NPC604854
0.5412 Remote Similarity NPC209846
0.5385 Remote Similarity NPC326592
0.5385 Remote Similarity NPC183950
0.5368 Remote Similarity NPC607513
0.5349 Remote Similarity NPC117418
0.5233 Remote Similarity NPC611357
0.5222 Remote Similarity NPC475942
0.5217 Remote Similarity NPC109594
0.5213 Remote Similarity NPC472607
0.52 Remote Similarity NPC256760
0.519 Remote Similarity NPC47781
0.5109 Remote Similarity NPC601144
0.5094 Remote Similarity NPC324742
0.5063 Remote Similarity NPC4455
0.5063 Remote Similarity NPC128863
0.5059 Remote Similarity NPC228383
0.5059 Remote Similarity NPC239644
0.505 Remote Similarity NPC195257

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC59717 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