Natural Product: NPC523850

Natural Product IDNPC523850
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Daidzein-7-(2-deoxy-alpha-L-fucopyranoside)
IUPAC Name 7-[(2~{S},4~{S},5~{S},6~{S})-4,5-dihydroxy-6-methyl-tetrahydropyran-2-yl]oxy-3-(4-hydroxyphenyl)chromen-4-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 IJFAWAIJDFHSKQ-XTXNGSAOSA-N
Standard InCHI InChI=1S/C21H20O7/c1-11-20(24)17(23)9-19(27-11)28-14-6-7-15-18(8-14)26-10-16(21(15)25)12-2-4-13(22)5-3-12/h2-8,10-11,17,19-20,22-24H,9H2,1H3/t11-,17-,19-,20+/m0/s1
SMILES C[C@@H]1O[C@@H](OC2=CC=C3C(=O)C(C4=CC=C(O)C=C4)=COC3=C2)C[C@H](O)[C@@H]1O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   384.12 Volume:   377.986
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Van der Waals volume.
Dense:   1.016 LogP:   1.35
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.672
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.762
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The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   24.0
TPSA:   109.36
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Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   3.0 Rings:   4.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.636 GASA:   0.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.635 Fsp3:   0.286
MCE-18:   77.519
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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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.561 Fluc inhibitor:   0.746
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.948
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.602
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.223 Promiscuous compounds:   0.636

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.085 MDCK Permeability:   -5.081
Pgp-inhibitor:   0.001 Pgp-substrate:   0.271
PAMPA:   0.992
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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):   0.088
20% Bioavailability (F20%):   0.662 30% Bioavailability (F30%):   0.676
50% Bioavailability (F50%):   0.939

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.004 MRP1:   0.709
Plasma Protein Binding (PPB):   91.824% Volume Distribution (VD):   -0.068
Fu: 9.944%
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The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.907
OATP1B3 inhibitor:   0.968 BCRP inhibitor:   0.142
BSEP inhibitor:   0.693

ADMET: Metabolism

CYP1A2-inhibitor:   0.395 CYP1A2-substrate:   0.943
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.839
CYP2C9-inhibitor:   0.951 CYP2C9-substrate:   0.886
CYP2D6-inhibitor:   0.728 CYP2D6-substrate:   0.018
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.999
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.002
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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):  5.184 Half-life (T1/2):  2.205

ADMET: Toxicity

hERG Blockers:  0.269 hERG Blockers (10um):  0.524
Human Hepatotoxicity (H-HT):  0.719 Drug-induced Liver Injury (DILI):  0.921
AMES Toxicity:  0.925 Rat Oral Acute Toxicity:  0.71
Maximum Recommended Daily Dose:  0.864 Skin Sensitization:  0.908
Carcinogencity:  0.596 Eye Corrosion:  0.0
Eye Irritation:  0.664 Respiratory Toxicity:  0.599
Drug-induced Neurotoxicity:  0.796 Ototoxicity:  0.588
Hematotoxicity:  0.361 Drug-induced Nephrotoxicity:  0.719
Genotoxicity:  0.978 RPMI-8226 Immunitoxicity:  0.179
A549 Cytotoxicity:  0.906 Hek293 Cytotoxicity:  0.794
BCF:   1.199
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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:   3.995
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.952
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.632
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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
NPO57035 Micromonospora aurantiaca 110B Genus Micromonosporaceae Bacteria n.a. n.a. n.a. Database[COCONUT]

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 NPC523850 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
0.7917 Intermediate Similarity NPC211014
0.6883 Remote Similarity NPC161749
0.6667 Remote Similarity NPC25547
0.6471 Remote Similarity NPC181124
0.6125 Remote Similarity NPC259070
0.5926 Remote Similarity NPC348541
0.5875 Remote Similarity NPC487214
0.561 Remote Similarity NPC45165
0.5581 Remote Similarity NPC43761
0.5402 Remote Similarity NPC229729
0.5294 Remote Similarity NPC105511
0.5278 Remote Similarity NPC605229
0.5238 Remote Similarity NPC160515
0.5205 Remote Similarity NPC479067
0.5161 Remote Similarity NPC303913
0.5155 Remote Similarity NPC231194
0.5116 Remote Similarity NPC197896
0.5116 Remote Similarity NPC258035
0.5116 Remote Similarity NPC313163
0.507 Remote Similarity NPC182428
0.5056 Remote Similarity NPC601607

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC523850 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
0.6883 Remote Similarity NPD4381 Clinical (unspecified phase)
0.5238 Remote Similarity NPD3818 Discontinued
0.5205 Remote Similarity NPD2796 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