Natural Product: NPC482736

Natural Product IDNPC482736
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
UQCQRSHWIVBHAZ-VZNIBWDRSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001766] Fatty acyl glycosides
          • [CHEMONTID:0002201] Sophorolipids

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 UQCQRSHWIVBHAZ-VZNIBWDRSA-N
Standard InCHI InChI=1S/C50H76O21/c1-20-29(54)31(56)35(60)41(65-20)70-37-32(57)30(55)25(19-51)67-42(37)71-38-34(59)33(58)36(40(61)62)69-43(38)68-27-11-12-48(7)26(45(27,3)4)10-13-50(9)39(48)24(53)16-22-23-17-46(5,44(63)64)18-28(66-21(2)52)47(23,6)14-15-49(22,50)8/h16,20,23,25-39,41-43,51,54-60H,10-15,17-19H2,1-9H3,(H,61,62)(H,63,64)/t20-,23+,25+,26-,27-,28+,29-,30+,31+,32-,33-,34+,35+,36+,37+,38-,39+,41-,42-,43-,46+,47+,48-,49+,50+/m1/s1
SMILES C[C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O[C@H]1[C@@H]([C@H]([C@H](CO)O[C@@H]1O[C@@H]1[C@H]([C@H]([C@@H](C(=O)O)O[C@H]1O[C@@H]1CC[C@]2(C)[C@H](CC[C@@]3(C)[C@H]2C(=O)C=C2[C@@H]4C[C@@](C)(C[C@@H]([C@@]4(C)CC[C@]32C)OC(=O)C)C(=O)O)C1(C)C)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1012.49 Volume:   976.317
?
Van der Waals volume.
Dense:   1.037 LogP:   1.058
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.646
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.366
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   11.0 Rigid Bonds:   48.0
TPSA:   335.19
?
Topological Polar Surface Area.
H-Bond Acceptor:   21.0
H-Bond Donor:   10.0 Rings:   8.0
Heavy Atoms:   21.0

MedChem Properties

QED Drug-Likeness Score:   0.105 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.569 Fsp3:   0.88
MCE-18:   182.468
?
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:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.785 Fluc inhibitor:   0.002
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.058
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.209 Promiscuous compounds:   0.33

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.417 MDCK Permeability:   -5.09
Pgp-inhibitor:   0.0 Pgp-substrate:   0.131
PAMPA:   1.0
?
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):   0.817
20% Bioavailability (F20%):   0.318 30% Bioavailability (F30%):   0.877
50% Bioavailability (F50%):   0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.338
Plasma Protein Binding (PPB):   55.605% Volume Distribution (VD):   -0.543
Fu: 30.552%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.778 BCRP inhibitor:   0.0
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   0.938
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.843
HLM stability:   0.0
?
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):  0.079 Half-life (T1/2):  3.522

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.001
Human Hepatotoxicity (H-HT):  0.611 Drug-induced Liver Injury (DILI):  0.99
AMES Toxicity:  0.402 Rat Oral Acute Toxicity:  0.013
Maximum Recommended Daily Dose:  0.004 Skin Sensitization:  1.0
Carcinogencity:  0.037 Eye Corrosion:  0.0
Eye Irritation:  0.003 Respiratory Toxicity:  0.01
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.995
Hematotoxicity:  0.543 Drug-induced Nephrotoxicity:  0.999
Genotoxicity:  0.903 RPMI-8226 Immunitoxicity:  0.232
A549 Cytotoxicity:  0.17 Hek293 Cytotoxicity:  0.034
BCF:   0.344
?
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:   3.636
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.667
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.482
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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
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11164-015-2099-x]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1134/S1021443711030101]
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]
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]
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]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[32196343]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
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]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
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]

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
NPT742 Organism Influenza A virus Influenza A virus Activity = 47.0 % PMID[26841168]
NPT742 Organism Influenza A virus Influenza A virus IC50 = 39600.0 nM PMID[26841168]

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 NPC482736 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 NPC482738
0.9208 High Similarity NPC482735
0.902 High Similarity NPC482737
0.8611 High Similarity NPC482739
0.819 Intermediate Similarity NPC482734
0.819 Intermediate Similarity NPC182342
0.819 Intermediate Similarity NPC482727
0.819 Intermediate Similarity NPC471964
0.7838 Intermediate Similarity NPC471962
0.7615 Intermediate Similarity NPC482755
0.6964 Remote Similarity NPC482722
0.6964 Remote Similarity NPC471963
0.6696 Remote Similarity NPC262199
0.6667 Remote Similarity NPC482744
0.6638 Remote Similarity NPC482740
0.6637 Remote Similarity NPC471965
0.6637 Remote Similarity NPC482749
0.6607 Remote Similarity NPC482747
0.6607 Remote Similarity NPC202666
0.6607 Remote Similarity NPC471961
0.6607 Remote Similarity NPC242015
0.6491 Remote Similarity NPC285091
0.6356 Remote Similarity NPC247315
0.6356 Remote Similarity NPC482728
0.6195 Remote Similarity NPC482750
0.6121 Remote Similarity NPC482741
0.6121 Remote Similarity NPC482745
0.6121 Remote Similarity NPC482743
0.6121 Remote Similarity NPC146753
0.605 Remote Similarity NPC131469
0.6034 Remote Similarity NPC482717
0.6 Remote Similarity NPC95437
0.6 Remote Similarity NPC471967
0.595 Remote Similarity NPC114692
0.5882 Remote Similarity NPC14617
0.5833 Remote Similarity NPC482729
0.5833 Remote Similarity NPC482742
0.5794 Remote Similarity NPC313110
0.5752 Remote Similarity NPC482752
0.5726 Remote Similarity NPC120116
0.5565 Remote Similarity NPC236657
0.5372 Remote Similarity NPC482746
0.5366 Remote Similarity NPC251768
0.5354 Remote Similarity NPC187618
0.5289 Remote Similarity NPC472949
0.5259 Remote Similarity NPC484061
0.5259 Remote Similarity NPC484062
0.525 Remote Similarity NPC25605
0.525 Remote Similarity NPC309780
0.5238 Remote Similarity NPC64715
0.52 Remote Similarity NPC118440
0.5182 Remote Similarity NPC258617
0.5156 Remote Similarity NPC301449
0.5156 Remote Similarity NPC477075
0.5156 Remote Similarity NPC477079
0.5156 Remote Similarity NPC601290
0.5116 Remote Similarity NPC477077
0.5116 Remote Similarity NPC477078
0.5039 Remote Similarity NPC477076
0.5038 Remote Similarity NPC151543

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC482736 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
0.6607 Remote Similarity NPD8328 Phase 2

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