Natural Product: NPC80427

Natural Product IDNPC80427
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XWIDINOKCRFVHQ-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5321435
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001615] Flavones
          • [CHEMONTID:0001136] Flavonols

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 XWIDINOKCRFVHQ-UHFFFAOYSA-N
Standard InCHI InChI=1S/C17H14O8/c1-23-10-5-7(3-4-8(10)18)16-15(22)13(20)12-11(25-16)6-9(19)17(24-2)14(12)21/h3-6,18-19,21-22H,1-2H3
SMILES COc1cc(ccc1O)c1c(c(=O)c2c(cc(c(c2O)OC)O)o1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   346.07 Volume:   326.149
?
Van der Waals volume.
Dense:   1.061 LogP:   1.665
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.799
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.701
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   18.0
TPSA:   129.59
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   4.0 Rings:   3.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.568 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.585 Fsp3:   0.118
MCE-18:   20.0
?
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:   1 PAINS Alert:   0
Colloidal aggregators:   0.807 Fluc inhibitor:   0.469
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.913
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.567
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.461 Promiscuous compounds:   0.904

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.37 MDCK Permeability:   -4.825
Pgp-inhibitor:   0.94 Pgp-substrate:   0.083
PAMPA:   0.076
?
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):   0.154
20% Bioavailability (F20%):   0.058 30% Bioavailability (F30%):   0.693
50% Bioavailability (F50%):   0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.827
Plasma Protein Binding (PPB):   97.683% Volume Distribution (VD):   -0.721
Fu: 2.659%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.995
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.999
BSEP inhibitor:   0.804

ADMET: Metabolism

CYP1A2-inhibitor:   0.95 CYP1A2-substrate:   0.332
CYP2C19-inhibitor:   0.006 CYP2C19-substrate:   0.744
CYP2C9-inhibitor:   0.362 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.987 CYP2D6-substrate:   0.955
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.002
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.995
HLM stability:   0.984
?
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):  3.202 Half-life (T1/2):  1.669

ADMET: Toxicity

hERG Blockers:  0.062 hERG Blockers (10um):  0.472
Human Hepatotoxicity (H-HT):  0.403 Drug-induced Liver Injury (DILI):  0.672
AMES Toxicity:  0.526 Rat Oral Acute Toxicity:  0.451
Maximum Recommended Daily Dose:  0.534 Skin Sensitization:  0.763
Carcinogencity:  0.627 Eye Corrosion:  0.403
Eye Irritation:  0.989 Respiratory Toxicity:  0.741
Drug-induced Neurotoxicity:  0.063 Ototoxicity:  0.158
Hematotoxicity:  0.163 Drug-induced Nephrotoxicity:  0.091
Genotoxicity:  0.582 RPMI-8226 Immunitoxicity:  0.084
A549 Cytotoxicity:  0.319 Hek293 Cytotoxicity:  0.428
BCF:   0.821
?
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:   3.47
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.277
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.749
?
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
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO17782 Inula britannica Species Asteraceae Eukaryota flowers n.a. n.a. PMID[16643020]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[24913660]
NPO9124 Inula japonica Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[27276091]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[35481430]
NPO10561 Mentha suaveolens Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36432812]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[37241749]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[37298924]
NPO10561 Mentha suaveolens Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37836777]
NPO10561 Mentha suaveolens Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38560258]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. leaf n.a. PMID[9433811]
NPO14052 Gliricidia sepium Species Fabaceae Eukaryota bark n.a. n.a. PMID[9917318]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14052 Gliricidia sepium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17476 Austrotaxus spicata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10561 Mentha suaveolens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9124 Inula japonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17782 Inula britannica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. Database[FooDB]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota Leaves n.a. Database[FooDB]
NPO27772 Flos inulae Species Lycaenidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17476 Austrotaxus spicata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17782 Inula britannica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9124 Inula japonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO9124 Inula japonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17782 Inula britannica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17476 Austrotaxus spicata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10561 Mentha suaveolens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27772 Flos inulae Species Lycaenidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17476 Austrotaxus spicata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9124 Inula japonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17782 Inula britannica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9124 Inula japonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17782 Inula britannica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9788 Coffea arabica Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9124 Inula japonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14052 Gliricidia sepium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10219 Juniperus communis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17782 Inula britannica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10561 Mentha suaveolens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14582 Spinacia oleracea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17476 Austrotaxus spicata Species Taxaceae 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 NPC80427 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
0.7885 Intermediate Similarity NPC98661
0.7679 Intermediate Similarity NPC227192
0.75 Intermediate Similarity NPC125062
0.7358 Intermediate Similarity NPC26227
0.7222 Intermediate Similarity NPC44079
0.7193 Intermediate Similarity NPC252933
0.7143 Intermediate Similarity NPC83508
0.6724 Remote Similarity NPC602125
0.6724 Remote Similarity NPC610401
0.661 Remote Similarity NPC604021
0.5763 Remote Similarity NPC241498
0.5763 Remote Similarity NPC284552
0.5763 Remote Similarity NPC266960
0.5667 Remote Similarity NPC100887
0.5667 Remote Similarity NPC28274
0.5667 Remote Similarity NPC163524
0.5645 Remote Similarity NPC93376
0.5593 Remote Similarity NPC472438
0.5574 Remote Similarity NPC312924
0.5556 Remote Similarity NPC183950
0.5556 Remote Similarity NPC279989
0.55 Remote Similarity NPC219330
0.5484 Remote Similarity NPC115798
0.5484 Remote Similarity NPC54394
0.5484 Remote Similarity NPC159103
0.5484 Remote Similarity NPC255350
0.541 Remote Similarity NPC50403
0.541 Remote Similarity NPC87125
0.541 Remote Similarity NPC143799
0.5397 Remote Similarity NPC4455
0.5397 Remote Similarity NPC288669
0.5333 Remote Similarity NPC293183
0.5323 Remote Similarity NPC9609
0.5323 Remote Similarity NPC49824
0.5323 Remote Similarity NPC256283
0.5312 Remote Similarity NPC261004
0.5312 Remote Similarity NPC133953
0.5312 Remote Similarity NPC47781
0.5312 Remote Similarity NPC137062
0.5312 Remote Similarity NPC78326
0.5246 Remote Similarity NPC203891
0.5246 Remote Similarity NPC156222
0.5238 Remote Similarity NPC200740
0.5238 Remote Similarity NPC280339
0.5238 Remote Similarity NPC29841
0.5238 Remote Similarity NPC166753
0.5195 Remote Similarity NPC101026
0.5195 Remote Similarity NPC488077
0.5161 Remote Similarity NPC241838
0.5156 Remote Similarity NPC18607
0.5156 Remote Similarity NPC236223
0.5156 Remote Similarity NPC115323
0.5156 Remote Similarity NPC609179
0.5132 Remote Similarity NPC475942
0.5079 Remote Similarity NPC32420
0.5077 Remote Similarity NPC19687
0.5077 Remote Similarity NPC227325
0.5077 Remote Similarity NPC606105
0.5063 Remote Similarity NPC601586

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC80427 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
0.5484 Remote Similarity NPD2801 Pre-clinical

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