Natural Product: NPC42346

Natural Product IDNPC42346
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 PMBOOVZSTMWOFS-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5496475
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002591] 6-O-methylated flavonoids

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 PMBOOVZSTMWOFS-UHFFFAOYSA-N
Standard InCHI InChI=1S/C18H16O8/c1-23-14-5-8(4-10(20)17(14)24-2)12-6-9(19)15-13(26-12)7-11(21)18(25-3)16(15)22/h4-7,20-22H,1-3H3
SMILES COc1cc(cc(c1OC)O)c1cc(=O)c2c(cc(c(c2O)OC)O)o1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   360.08 Volume:   343.445
?
Van der Waals volume.
Dense:   1.048 LogP:   2.132
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.116
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.435
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   18.0
TPSA:   118.59
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.65 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.632 Fsp3:   0.167
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:   0.598 Fluc inhibitor:   0.579
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.87
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.688
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.435 Promiscuous compounds:   0.842

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.177 MDCK Permeability:   -4.79
Pgp-inhibitor:   0.352 Pgp-substrate:   0.443
PAMPA:   0.048
?
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):   0.013
20% Bioavailability (F20%):   0.132 30% Bioavailability (F30%):   0.522
50% Bioavailability (F50%):   0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.029 MRP1:   0.88
Plasma Protein Binding (PPB):   95.112% Volume Distribution (VD):   -0.438
Fu: 6.233%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.97
OATP1B3 inhibitor:   0.996 BCRP inhibitor:   0.972
BSEP inhibitor:   0.521

ADMET: Metabolism

CYP1A2-inhibitor:   0.961 CYP1A2-substrate:   0.428
CYP2C19-inhibitor:   0.002 CYP2C19-substrate:   0.007
CYP2C9-inhibitor:   0.957 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.999 CYP2D6-substrate:   0.985
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   0.001
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.997
HLM stability:   0.659
?
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):  4.008 Half-life (T1/2):  1.259

ADMET: Toxicity

hERG Blockers:  0.063 hERG Blockers (10um):  0.464
Human Hepatotoxicity (H-HT):  0.398 Drug-induced Liver Injury (DILI):  0.583
AMES Toxicity:  0.469 Rat Oral Acute Toxicity:  0.434
Maximum Recommended Daily Dose:  0.624 Skin Sensitization:  0.741
Carcinogencity:  0.619 Eye Corrosion:  0.539
Eye Irritation:  0.992 Respiratory Toxicity:  0.801
Drug-induced Neurotoxicity:  0.104 Ototoxicity:  0.15
Hematotoxicity:  0.187 Drug-induced Nephrotoxicity:  0.099
Genotoxicity:  0.663 RPMI-8226 Immunitoxicity:  0.106
A549 Cytotoxicity:  0.334 Hek293 Cytotoxicity:  0.513
BCF:   0.742
?
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:   3.221
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.312
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.724
?
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
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jep.2005.01.054]
NPO10304 Colletotrichum gloeosporioides Species Glomerellaceae Eukaryota Artemisia mongolica n.a. n.a. PMID[11087599]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO10304 Colletotrichum gloeosporioides Species Glomerellaceae Eukaryota n.a. n.a. n.a. PMID[29035525]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31181920]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31418264]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[31444719]
NPO5118 Zanthoxylum myriacanthum Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[36627746]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38754641]
NPO7968 Artemisia kurramensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9447 Tolypothrix tenuis Species Tolypothrichaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9265 Jasonia candicans Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO540 Anaphalis araneosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10536 Rhabdonia verticillata Species Areschougiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10304 Colletotrichum gloeosporioides Species Glomerellaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11583 Calycanthus floridus Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1252 Aglaia grandis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26396 Coprinopsis atramentaria Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5118 Zanthoxylum myriacanthum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11583 Calycanthus floridus Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5118 Zanthoxylum myriacanthum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26719 Tetrapanax papyrifer Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1252 Aglaia grandis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11583 Calycanthus floridus Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11452 Pterocarpus officinalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26396 Coprinopsis atramentaria Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11583 Calycanthus floridus Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8120 Episcia cupreata Species Gesneriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9265 Jasonia candicans Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5118 Zanthoxylum myriacanthum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11544 Vernonia lanuginosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12613 Catunaregam tomentosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7779 Impatiens edgeworthii Species Balsaminaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10081 Othonna sedifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO557 Bhesa nitidissima Species Centroplacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10304 Colletotrichum gloeosporioides Species Glomerellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26719 Tetrapanax papyrifer Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12153 Adenia globosa Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7968 Artemisia kurramensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7463 Ranzania japonica Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9447 Tolypothrix tenuis Species Tolypothrichaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO10536 Rhabdonia verticillata Species Areschougiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28276 Artemisia argyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11583 Calycanthus floridus Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11452 Pterocarpus officinalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO540 Anaphalis araneosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6802 Rothmannia wittii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26396 Coprinopsis atramentaria Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10798 Cis punctifer Species Ciidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10483 Chrysanthemum sinense Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1252 Aglaia grandis Species Meliaceae 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 NPC42346 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
0.7593 Intermediate Similarity NPC255350
0.7455 Intermediate Similarity NPC606638
0.7407 Intermediate Similarity NPC256283
0.7358 Intermediate Similarity NPC284552
0.7273 Intermediate Similarity NPC29841
0.7222 Intermediate Similarity NPC100887
0.717 Intermediate Similarity NPC293183
0.7037 Intermediate Similarity NPC241498
0.7037 Intermediate Similarity NPC156222
0.6964 Remote Similarity NPC83508
0.6842 Remote Similarity NPC177298
0.6508 Remote Similarity NPC213622
0.625 Remote Similarity NPC75279
0.6094 Remote Similarity NPC470402
0.6034 Remote Similarity NPC62536
0.6034 Remote Similarity NPC601901
0.6 Remote Similarity NPC160951
0.6 Remote Similarity NPC609179
0.5965 Remote Similarity NPC472438
0.5932 Remote Similarity NPC208197
0.5862 Remote Similarity NPC98661
0.5833 Remote Similarity NPC39732
0.5833 Remote Similarity NPC69394
0.5833 Remote Similarity NPC60972
0.5763 Remote Similarity NPC276409
0.5738 Remote Similarity NPC474520
0.5738 Remote Similarity NPC162351
0.569 Remote Similarity NPC26227
0.5667 Remote Similarity NPC25270
0.5645 Remote Similarity NPC47781
0.5593 Remote Similarity NPC44079
0.5593 Remote Similarity NPC239128
0.5574 Remote Similarity NPC250557
0.5574 Remote Similarity NPC115798
0.55 Remote Similarity NPC33265
0.55 Remote Similarity NPC145379
0.55 Remote Similarity NPC120163
0.5484 Remote Similarity NPC78302
0.5484 Remote Similarity NPC52005
0.5484 Remote Similarity NPC12200
0.5424 Remote Similarity NPC250822
0.541 Remote Similarity NPC9609
0.5333 Remote Similarity NPC609062
0.5246 Remote Similarity NPC120464
0.5246 Remote Similarity NPC163524
0.5246 Remote Similarity NPC483773
0.5238 Remote Similarity NPC235215
0.5238 Remote Similarity NPC206604
0.5161 Remote Similarity NPC163780
0.5156 Remote Similarity NPC183950
0.5082 Remote Similarity NPC203891
0.5082 Remote Similarity NPC266960
0.5079 Remote Similarity NPC183597
0.5079 Remote Similarity NPC146165
0.5079 Remote Similarity NPC212678

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC42346 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
0.7593 Intermediate 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