Natural Product: NPC232292

Natural Product IDNPC232292
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 GSZUGBAEBARHAW-UCYAAXKESA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44257572
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-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 GSZUGBAEBARHAW-UCYAAXKESA-N
Standard InCHI InChI=1S/C21H20O9/c22-9-17-18(25)19(26)20(27)21(30-17)28-12-4-1-10(2-5-12)15-8-14(24)13-6-3-11(23)7-16(13)29-15/h1-8,17-23,25-27H,9H2/t17?,18-,19?,20?,21-/m1/s1
SMILES c1cc(ccc1c1cc(=O)c2ccc(cc2o1)O)O[C@H]1C(C([C@@H](C(CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   416.11 Volume:   395.567
?
Van der Waals volume.
Dense:   1.052 LogP:   0.547
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.263
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.354
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   24.0
TPSA:   149.82
?
Topological Polar Surface Area.
 H-Bond Acceptor:   9.0
H-Bond Donor:   5.0 Rings:   4.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.406 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.635 Fsp3:   0.286
MCE-18:   80.889
?
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:   0.582 Fluc inhibitor:   0.452
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.984
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.841
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.295 Promiscuous compounds:   0.223

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.324 MDCK Permeability:   -5.115
Pgp-inhibitor:   0.0 Pgp-substrate:   0.946
PAMPA:   0.998
?
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):   0.68
20% Bioavailability (F20%):   0.88 30% Bioavailability (F30%):   0.988
50% Bioavailability (F50%):   0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.008 MRP1:   0.773
Plasma Protein Binding (PPB):   85.246% Volume Distribution (VD):   -0.035
Fu: 14.841%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.484
OATP1B3 inhibitor:   0.992 BCRP inhibitor:   0.297
BSEP inhibitor:   0.052

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.042 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.994 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.055 CYP2D6-substrate:   0.189
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.022
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.999
HLM stability:   0.004
?
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):  2.938 Half-life (T1/2):  3.027

ADMET: Toxicity

hERG Blockers:  0.078 hERG Blockers (10um):  0.242
Human Hepatotoxicity (H-HT):  0.571 Drug-induced Liver Injury (DILI):  0.803
AMES Toxicity:  0.783 Rat Oral Acute Toxicity:  0.188
Maximum Recommended Daily Dose:  0.407 Skin Sensitization:  0.322
Carcinogencity:  0.533 Eye Corrosion:  0.0
Eye Irritation:  0.415 Respiratory Toxicity:  0.073
Drug-induced Neurotoxicity:  0.03 Ototoxicity:  0.775
Hematotoxicity:  0.085 Drug-induced Nephrotoxicity:  0.106
Genotoxicity:  0.956 RPMI-8226 Immunitoxicity:  0.072
A549 Cytotoxicity:  0.104 Hek293 Cytotoxicity:  0.682
BCF:   0.506
?
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:   3.244
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.829
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.918
?
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
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11164-015-2099-x]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s40502-015-0143-x]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1093/pcp/pcg054]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1134/S1021443709050069]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1134/S1021443711030101]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota Leaves n.a. n.a. PMID[12713396]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. root n.a. PMID[16441081]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16675659]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota roots n.a. n.a. PMID[20022509]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21123068]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21866899]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. root n.a. PMID[22074222]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22074222]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[23325115]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota Roots n.a. n.a. PMID[23541646]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. rhizome n.a. PMID[23867078]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. root n.a. PMID[23867078]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24479468]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota roots n.a. n.a. PMID[24957203]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25445757]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25744461]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[26841168]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[28140583]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[28522265]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[29641206]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[32196343]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[39683057]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[7381508]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23019 Glycyrrhiza kansuensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27572 Sophora subprostrata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23019 Glycyrrhiza kansuensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27572 Sophora subprostrata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23019 Glycyrrhiza kansuensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27572 Sophora subprostrata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23019 Glycyrrhiza kansuensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27572 Sophora subprostrata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29384 Glycyrrhiza glabra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1698 Glycyrrhiza inflata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27572 Sophora subprostrata Species Fabaceae 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 NPC232292 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
0.7534 Intermediate Similarity NPC143851
0.6974 Remote Similarity NPC168822
0.6974 Remote Similarity NPC258035
0.6842 Remote Similarity NPC58053
0.6667 Remote Similarity NPC186807
0.6623 Remote Similarity NPC83283
0.6538 Remote Similarity NPC95090
0.6538 Remote Similarity NPC27408
0.6418 Remote Similarity NPC266597
0.641 Remote Similarity NPC39360
0.641 Remote Similarity NPC29763
0.641 Remote Similarity NPC210003
0.6296 Remote Similarity NPC191306
0.625 Remote Similarity NPC105025
0.625 Remote Similarity NPC610763
0.6235 Remote Similarity NPC603300
0.6145 Remote Similarity NPC88023
0.6145 Remote Similarity NPC206123
0.6145 Remote Similarity NPC309025
0.6125 Remote Similarity NPC93337
0.6125 Remote Similarity NPC64305
0.6125 Remote Similarity NPC146792
0.6024 Remote Similarity NPC601710
0.5926 Remote Similarity NPC189142
0.5926 Remote Similarity NPC77660
0.5904 Remote Similarity NPC609451
0.5833 Remote Similarity NPC22832
0.5833 Remote Similarity NPC243930
0.5833 Remote Similarity NPC605067
0.5802 Remote Similarity NPC261866
0.5802 Remote Similarity NPC45618
0.5783 Remote Similarity NPC222936
0.5783 Remote Similarity NPC472459
0.5783 Remote Similarity NPC201292
0.5765 Remote Similarity NPC607707
0.5732 Remote Similarity NPC259152
0.5663 Remote Similarity NPC58716
0.5663 Remote Similarity NPC100818
0.5663 Remote Similarity NPC45638
0.5647 Remote Similarity NPC601144
0.561 Remote Similarity NPC289667
0.5595 Remote Similarity NPC182045
0.5581 Remote Similarity NPC311830
0.5581 Remote Similarity NPC602805
0.5542 Remote Similarity NPC161749
0.5542 Remote Similarity NPC156457
0.5484 Remote Similarity NPC124155
0.5479 Remote Similarity NPC604422
0.5479 Remote Similarity NPC607642
0.5455 Remote Similarity NPC600870
0.5422 Remote Similarity NPC77672
0.5422 Remote Similarity NPC133671
0.5422 Remote Similarity NPC135391
0.5422 Remote Similarity NPC78263
0.5422 Remote Similarity NPC250069
0.5412 Remote Similarity NPC21100
0.5373 Remote Similarity NPC172262
0.5357 Remote Similarity NPC145038
0.5357 Remote Similarity NPC56077
0.5357 Remote Similarity NPC281131
0.5357 Remote Similarity NPC253662
0.5357 Remote Similarity NPC179950
0.5357 Remote Similarity NPC323593
0.5357 Remote Similarity NPC88789
0.5357 Remote Similarity NPC203500
0.5357 Remote Similarity NPC491374
0.5357 Remote Similarity NPC609879
0.5349 Remote Similarity NPC60735
0.5349 Remote Similarity NPC26230
0.5301 Remote Similarity NPC331652
0.5294 Remote Similarity NPC181712
0.5294 Remote Similarity NPC57601
0.5287 Remote Similarity NPC284960
0.5287 Remote Similarity NPC120099
0.5287 Remote Similarity NPC609478
0.5238 Remote Similarity NPC110349
0.5233 Remote Similarity NPC27942
0.5233 Remote Similarity NPC138540
0.5233 Remote Similarity NPC599850
0.5222 Remote Similarity NPC472607
0.5208 Remote Similarity NPC477629
0.5176 Remote Similarity NPC297987
0.5176 Remote Similarity NPC277205
0.5176 Remote Similarity NPC37919
0.5172 Remote Similarity NPC479401
0.5172 Remote Similarity NPC285197
0.5119 Remote Similarity NPC45165
0.5116 Remote Similarity NPC84265
0.5116 Remote Similarity NPC24043
0.5116 Remote Similarity NPC488080
0.5116 Remote Similarity NPC169977
0.5114 Remote Similarity NPC148710
0.5114 Remote Similarity NPC197285
0.5114 Remote Similarity NPC486578
0.5111 Remote Similarity NPC211594
0.5075 Remote Similarity NPC142319
0.5067 Remote Similarity NPC115323
0.5059 Remote Similarity NPC19388
0.5059 Remote Similarity NPC240431
0.5059 Remote Similarity NPC55786
0.5057 Remote Similarity NPC117260
0.5056 Remote Similarity NPC136761
0.5055 Remote Similarity NPC8856
0.5054 Remote Similarity NPC65003
0.5054 Remote Similarity NPC607513
0.5053 Remote Similarity NPC477628
0.5052 Remote Similarity NPC256760
0.5052 Remote Similarity NPC76831

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC232292 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
0.5542 Remote Similarity NPD4381 Clinical (unspecified phase)

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