Natural Product: NPC307938

Natural Product IDNPC307938
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Morin-7-O-Beta-D-Glucopyranoside
IUPAC Name 2-(2,4-dihydroxyphenyl)-3,5-dihydroxy-7-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxychromen-4-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL560178
PubChem CID 45269053
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0003533] Flavonoid-7-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 BCWBZRHEHFRQGI-HMGRVEAOSA-N
Standard InCHI InChI=1S/C21H20O12/c22-6-13-15(26)17(28)19(30)21(33-13)31-8-4-11(25)14-12(5-8)32-20(18(29)16(14)27)9-2-1-7(23)3-10(9)24/h1-5,13,15,17,19,21-26,28-30H,6H2/t13-,15-,17+,19-,21-/m1/s1
SMILES OC[C@H]1O[C@@H](Oc2cc(O)c3c(c2)oc(c(c3=O)O)c2ccc(cc2O)O)[C@@H]([C@H]([C@@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   464.1 Volume:   421.937
?
Van der Waals volume.
Dense:   1.1 LogP:   0.592
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.11
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.825
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   24.0
TPSA:   210.51
?
Topological Polar Surface Area.
 H-Bond Acceptor:   12.0
H-Bond Donor:   8.0 Rings:   4.0
Heavy Atoms:   12.0

MedChem Properties

QED Drug-Likeness Score:   0.245 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.063 Fsp3:   0.286
MCE-18:   91.0
?
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:   0.658 Fluc inhibitor:   0.323
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.909
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.774
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.298 Promiscuous compounds:   0.724

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.343 MDCK Permeability:   -4.903
Pgp-inhibitor:   0.002 Pgp-substrate:   0.448
PAMPA:   0.991
?
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):   0.873
20% Bioavailability (F20%):   0.05 30% Bioavailability (F30%):   0.991
50% Bioavailability (F50%):   0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.359
Plasma Protein Binding (PPB):   87.243% Volume Distribution (VD):   -0.167
Fu: 10.821%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.999
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.67
BSEP inhibitor:   0.002

ADMET: Metabolism

CYP1A2-inhibitor:   0.002 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.007
CYP2C9-inhibitor:   0.001 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.531
HLM stability:   0.187
?
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):  2.469 Half-life (T1/2):  4.449

ADMET: Toxicity

hERG Blockers:  0.013 hERG Blockers (10um):  0.107
Human Hepatotoxicity (H-HT):  0.585 Drug-induced Liver Injury (DILI):  0.95
AMES Toxicity:  0.887 Rat Oral Acute Toxicity:  0.044
Maximum Recommended Daily Dose:  0.093 Skin Sensitization:  0.99
Carcinogencity:  0.308 Eye Corrosion:  0.0
Eye Irritation:  0.727 Respiratory Toxicity:  0.041
Drug-induced Neurotoxicity:  0.001 Ototoxicity:  0.77
Hematotoxicity:  0.088 Drug-induced Nephrotoxicity:  0.265
Genotoxicity:  0.957 RPMI-8226 Immunitoxicity:  0.093
A549 Cytotoxicity:  0.417 Hek293 Cytotoxicity:  0.574
BCF:   0.484
?
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:   2.942
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.284
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.626
?
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
NPO594 Alpinia densespicata Species Staphylinidae Eukaryota n.a. n.a. n.a. PMID[19555124]
NPO594 Alpinia densespicata Species Staphylinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO594 Alpinia densespicata Species Staphylinidae 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
NPT113 Cell line RAW264.7 Mus musculus IC50 = 39100.0 nM PMID[19555124]
NPT113 Cell line RAW264.7 Mus musculus Activity > 80.0 % PMID[19555124]
NPT1 Others Radical scavenging activity n.a. ED50 = 22.2 uM PMID[19555124]

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 NPC307938 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
0.8219 Intermediate Similarity NPC323593
0.8219 Intermediate Similarity NPC203500
0.7733 Intermediate Similarity NPC277205
0.7733 Intermediate Similarity NPC37919
0.7215 Intermediate Similarity NPC285197
0.716 Intermediate Similarity NPC601586
0.6923 Remote Similarity NPC108831
0.6923 Remote Similarity NPC182634
0.6914 Remote Similarity NPC486578
0.6709 Remote Similarity NPC39360
0.6709 Remote Similarity NPC29763
0.6709 Remote Similarity NPC210003
0.6625 Remote Similarity NPC297987
0.6585 Remote Similarity NPC80140
0.65 Remote Similarity NPC238376
0.6341 Remote Similarity NPC84265
0.631 Remote Similarity NPC197285
0.6296 Remote Similarity NPC261866
0.625 Remote Similarity NPC275454
0.6235 Remote Similarity NPC116458
0.6235 Remote Similarity NPC246943
0.622 Remote Similarity NPC136042
0.622 Remote Similarity NPC189142
0.622 Remote Similarity NPC77660
0.6145 Remote Similarity NPC84362
0.6118 Remote Similarity NPC601144
0.6098 Remote Similarity NPC289667
0.6071 Remote Similarity NPC21100
0.6024 Remote Similarity NPC197896
0.6024 Remote Similarity NPC95090
0.6024 Remote Similarity NPC313163
0.6024 Remote Similarity NPC27408
0.5952 Remote Similarity NPC245014
0.593 Remote Similarity NPC243930
0.5882 Remote Similarity NPC117260
0.5862 Remote Similarity NPC311830
0.5862 Remote Similarity NPC605784
0.5862 Remote Similarity NPC607707
0.5823 Remote Similarity NPC191154
0.5806 Remote Similarity NPC479403
0.5747 Remote Similarity NPC22832
0.5714 Remote Similarity NPC67105
0.5699 Remote Similarity NPC64425
0.567 Remote Similarity NPC135358
0.5647 Remote Similarity NPC282987
0.5647 Remote Similarity NPC234739
0.5647 Remote Similarity NPC609879
0.5625 Remote Similarity NPC80068
0.5595 Remote Similarity NPC331652
0.5556 Remote Similarity NPC134819
0.5529 Remote Similarity NPC249281
0.5529 Remote Similarity NPC77672
0.5529 Remote Similarity NPC133671
0.5529 Remote Similarity NPC135391
0.5529 Remote Similarity NPC78263
0.5529 Remote Similarity NPC250069
0.5495 Remote Similarity NPC251417
0.5484 Remote Similarity NPC183672
0.5417 Remote Similarity NPC35119
0.5402 Remote Similarity NPC46420
0.5402 Remote Similarity NPC73511
0.5376 Remote Similarity NPC227508
0.5349 Remote Similarity NPC254306
0.5349 Remote Similarity NPC143851
0.5341 Remote Similarity NPC27942
0.5333 Remote Similarity NPC136761
0.5333 Remote Similarity NPC479406
0.5319 Remote Similarity NPC479405
0.5294 Remote Similarity NPC480796
0.5287 Remote Similarity NPC145038
0.5287 Remote Similarity NPC93337
0.5287 Remote Similarity NPC56077
0.5287 Remote Similarity NPC281131
0.5287 Remote Similarity NPC64305
0.5287 Remote Similarity NPC253662
0.5287 Remote Similarity NPC146792
0.5287 Remote Similarity NPC179950
0.5287 Remote Similarity NPC88789
0.5287 Remote Similarity NPC491374
0.5263 Remote Similarity NPC479404
0.5258 Remote Similarity NPC32641
0.5258 Remote Similarity NPC256188
0.5243 Remote Similarity NPC25523
0.5227 Remote Similarity NPC22195
0.5227 Remote Similarity NPC24043
0.5227 Remote Similarity NPC21190
0.5227 Remote Similarity NPC105025
0.5227 Remote Similarity NPC610763
0.5222 Remote Similarity NPC601710
0.52 Remote Similarity NPC143799
0.5172 Remote Similarity NPC476405
0.5172 Remote Similarity NPC19709
0.5172 Remote Similarity NPC83283
0.5169 Remote Similarity NPC472459
0.5169 Remote Similarity NPC138540
0.5161 Remote Similarity NPC8856
0.5158 Remote Similarity NPC65003
0.5114 Remote Similarity NPC8573
0.5109 Remote Similarity NPC276377
0.5104 Remote Similarity NPC131745
0.51 Remote Similarity NPC287889
0.5096 Remote Similarity NPC164704
0.5068 Remote Similarity NPC216361
0.5056 Remote Similarity NPC271692
0.5056 Remote Similarity NPC488080
0.5056 Remote Similarity NPC169977
0.5053 Remote Similarity NPC44931

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC307938 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