Natural Product: NPC587074

Natural Product IDNPC587074
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 [(2~{S},3~{S},4~{S},5~{R},6~{S})-3,4,5-trihydroxy-6-[5-hydroxy-3-(4-hydroxyphenyl)-4-oxo-chromen-7-yl]oxy-tetrahydropyran-2-yl]methyl acetate
IUPAC Name [(2~{S},3~{S},4~{S},5~{R},6~{S})-3,4,5-trihydroxy-6-[5-hydroxy-3-(4-hydroxyphenyl)-4-oxo-chromen-7-yl]oxy-tetrahydropyran-2-yl]methyl acetate
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 DXWGBJJLEDQBKS-LQLJJDJVSA-N
Standard InCHI InChI=1S/C23H22O11/c1-10(24)31-9-17-20(28)21(29)22(30)23(34-17)33-13-6-15(26)18-16(7-13)32-8-14(19(18)27)11-2-4-12(25)5-3-11/h2-8,17,20-23,25-26,28-30H,9H2,1H3/t17-,20+,21-,22+,23+/m0/s1
SMILES CC(=O)OC[C@@H]1O[C@@H](OC2=CC(O)=C3C(=O)C(C4=CC=C(O)C=C4)=COC3=C2)[C@H](O)[C@@H](O)[C@@H]1O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   474.12 Volume:   445.103
?
Van der Waals volume.
Dense:   1.065 LogP:   0.746
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.12
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.526
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   25.0
TPSA:   176.12
?
Topological Polar Surface Area.
 H-Bond Acceptor:   11.0
H-Bond Donor:   5.0 Rings:   4.0
Heavy Atoms:   11.0

MedChem Properties

QED Drug-Likeness Score:   0.328 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.912 Fsp3:   0.304
MCE-18:   86.667
?
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:   0.556 Fluc inhibitor:   0.284
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.81
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.895
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.054 Promiscuous compounds:   0.427

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.112 MDCK Permeability:   -5.146
Pgp-inhibitor:   0.0 Pgp-substrate:   0.595
PAMPA:   0.999
?
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):   0.746
20% Bioavailability (F20%):   0.869 30% Bioavailability (F30%):   0.989
50% Bioavailability (F50%):   0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.007 MRP1:   0.272
Plasma Protein Binding (PPB):   85.75% Volume Distribution (VD):   -0.1
Fu: 16.154%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.956
OATP1B3 inhibitor:   0.936 BCRP inhibitor:   0.18
BSEP inhibitor:   0.023

ADMET: Metabolism

CYP1A2-inhibitor:   0.592 CYP1A2-substrate:   0.001
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.055 CYP2C9-substrate:   0.249
CYP2D6-inhibitor:   0.006 CYP2D6-substrate:   0.038
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.858
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.39
HLM stability:   0.002
?
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):  1.91 Half-life (T1/2):  2.363

ADMET: Toxicity

hERG Blockers:  0.026 hERG Blockers (10um):  0.185
Human Hepatotoxicity (H-HT):  0.561 Drug-induced Liver Injury (DILI):  0.984
AMES Toxicity:  0.933 Rat Oral Acute Toxicity:  0.133
Maximum Recommended Daily Dose:  0.145 Skin Sensitization:  0.98
Carcinogencity:  0.301 Eye Corrosion:  0.0
Eye Irritation:  0.48 Respiratory Toxicity:  0.06
Drug-induced Neurotoxicity:  0.079 Ototoxicity:  0.658
Hematotoxicity:  0.258 Drug-induced Nephrotoxicity:  0.715
Genotoxicity:  0.961 RPMI-8226 Immunitoxicity:  0.137
A549 Cytotoxicity:  0.745 Hek293 Cytotoxicity:  0.492
BCF:   0.583
?
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:   3.266
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.57
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.056
?
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
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. Wrocław, Poland 2004–2005 DOI[10.1016/J.FOODCHEM.2006.08.014]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0021-9258(18)90865-3]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0168-9452(02)00136-X]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0168-9452(02)00136-X]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/jf950732o]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1023/A:1024390522259]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[10775096]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. root n.a. PMID[1622242]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16659156]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16668466]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[20963508]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO7635 Glycine max Species Fabaceae Eukaryota Seeds Tekirdag, Turkey PMID[24499198]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25053043]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25070365]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. seed n.a. PMID[25369450]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25369450]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Testa n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Hypocotyl n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Cotyledon n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. seed n.a. Database[MetaboLights]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO7635 Glycine max Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7635 Glycine max 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 NPC587074 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
0.8272 Intermediate Similarity NPC303913
0.8049 Intermediate Similarity NPC479405
0.7952 Intermediate Similarity NPC479404
0.7895 Intermediate Similarity NPC348541
0.7564 Intermediate Similarity NPC197896
0.7564 Intermediate Similarity NPC313163
0.7089 Intermediate Similarity NPC160515
0.6778 Remote Similarity NPC479403
0.6627 Remote Similarity NPC73511
0.6395 Remote Similarity NPC610187
0.6386 Remote Similarity NPC211014
0.6292 Remote Similarity NPC487212
0.6279 Remote Similarity NPC80140
0.6118 Remote Similarity NPC161749
0.6118 Remote Similarity NPC234739
0.6081 Remote Similarity NPC303644
0.5814 Remote Similarity NPC259070
0.5795 Remote Similarity NPC205076
0.5789 Remote Similarity NPC64051
0.5773 Remote Similarity NPC270675
0.5773 Remote Similarity NPC195685
0.5747 Remote Similarity NPC487213
0.5714 Remote Similarity NPC80068
0.5714 Remote Similarity NPC231194
0.5667 Remote Similarity NPC226722
0.5652 Remote Similarity NPC477848
0.5638 Remote Similarity NPC44931
0.5618 Remote Similarity NPC100720
0.56 Remote Similarity NPC472994
0.5568 Remote Similarity NPC105511
0.5568 Remote Similarity NPC156457
0.5521 Remote Similarity NPC186816
0.551 Remote Similarity NPC51326
0.55 Remote Similarity NPC101636
0.55 Remote Similarity NPC298171
0.5484 Remote Similarity NPC172807
0.5385 Remote Similarity NPC480796
0.5385 Remote Similarity NPC472993
0.5349 Remote Similarity NPC25547
0.5347 Remote Similarity NPC235575
0.534 Remote Similarity NPC121703
0.5333 Remote Similarity NPC192229
0.5325 Remote Similarity NPC116632
0.5306 Remote Similarity NPC46202
0.53 Remote Similarity NPC488089
0.5281 Remote Similarity NPC108831
0.5281 Remote Similarity NPC182634
0.5258 Remote Similarity NPC22062
0.5258 Remote Similarity NPC473634
0.5258 Remote Similarity NPC475155
0.5258 Remote Similarity NPC138811
0.5213 Remote Similarity NPC53587
0.52 Remote Similarity NPC229409
0.52 Remote Similarity NPC72016
0.5169 Remote Similarity NPC331652
0.5161 Remote Similarity NPC43761
0.5158 Remote Similarity NPC116864
0.5158 Remote Similarity NPC244776
0.5158 Remote Similarity NPC211594
0.5155 Remote Similarity NPC67105
0.5149 Remote Similarity NPC294722
0.5111 Remote Similarity NPC249281
0.5109 Remote Similarity NPC27942
0.5109 Remote Similarity NPC138540
0.5102 Remote Similarity NPC210073
0.5059 Remote Similarity NPC249824
0.5055 Remote Similarity NPC258035
0.5055 Remote Similarity NPC323593
0.5055 Remote Similarity NPC203500
0.5053 Remote Similarity NPC276377
0.505 Remote Similarity NPC473623
0.505 Remote Similarity NPC209296
0.505 Remote Similarity NPC257714

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC587074 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
0.6118 Remote Similarity NPD4381 Clinical (unspecified phase)
0.505 Remote Similarity NPD7054 Phase 4

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