Natural Product: NPC165302

Natural Product IDNPC165302
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 VXXKDWBEVHGANN-YYMOATHLSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 102021737
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic 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 VXXKDWBEVHGANN-YYMOATHLSA-N
Standard InCHI InChI=1S/C16H24O9/c1-23-11-5-10(3-2-8(11)4-9(19)6-17)24-16-15(22)14(21)13(20)12(7-18)25-16/h2-3,5,9,12-22H,4,6-7H2,1H3/t9-,12-,13-,14+,15-,16-/m1/s1
SMILES COc1cc(ccc1C[C@H](CO)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   360.14 Volume:   339.382
?
Van der Waals volume.
Dense:   1.061 LogP:   -0.399
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.138
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.287
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   12.0
TPSA:   149.07
?
Topological Polar Surface Area.
 H-Bond Acceptor:   9.0
H-Bond Donor:   6.0 Rings:   2.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.318 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.74 Fsp3:   0.625
MCE-18:   50.769
?
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:   0.527 Fluc inhibitor:   0.011
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.053
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.034
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.209 Promiscuous compounds:   0.026

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.421 MDCK Permeability:   -5.102
Pgp-inhibitor:   0.0 Pgp-substrate:   0.374
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):   0.045
20% Bioavailability (F20%):   0.022 30% Bioavailability (F30%):   0.667
50% Bioavailability (F50%):   0.771

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.008 MRP1:   0.012
Plasma Protein Binding (PPB):   53.288% Volume Distribution (VD):   -0.363
Fu: 46.861%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.056
BSEP inhibitor:   0.004

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.007 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:   0.001
HLM stability:   0.003
?
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):  2.279 Half-life (T1/2):  3.316

ADMET: Toxicity

hERG Blockers:  0.022 hERG Blockers (10um):  0.034
Human Hepatotoxicity (H-HT):  0.531 Drug-induced Liver Injury (DILI):  0.126
AMES Toxicity:  0.898 Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.003 Skin Sensitization:  0.995
Carcinogencity:  0.188 Eye Corrosion:  0.0
Eye Irritation:  0.22 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.002 Ototoxicity:  0.99
Hematotoxicity:  0.211 Drug-induced Nephrotoxicity:  0.816
Genotoxicity:  0.011 RPMI-8226 Immunitoxicity:  0.063
A549 Cytotoxicity:  0.015 Hek293 Cytotoxicity:  0.041
BCF:   0.17
?
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:   2.264
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.896
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.99
?
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
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. seed n.a. PMID[21049975]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. aerial part n.a. PMID[25154406]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[30551419]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[35999251]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[36432786]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[36840093]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[37653914]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[38592874]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[38719900]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[39065713]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[39683666]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21460 Anethum graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21460 Anethum graveolens Species Apiaceae 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 NPC165302 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
0.6491 Remote Similarity NPC218685
0.6379 Remote Similarity NPC472024
0.6182 Remote Similarity NPC60589
0.6182 Remote Similarity NPC469708
0.6111 Remote Similarity NPC153149
0.6038 Remote Similarity NPC276195
0.6038 Remote Similarity NPC212729
0.6038 Remote Similarity NPC604498
0.6 Remote Similarity NPC25817
0.5938 Remote Similarity NPC479030
0.5926 Remote Similarity NPC217854
0.5926 Remote Similarity NPC269242
0.5893 Remote Similarity NPC609376
0.5833 Remote Similarity NPC479028
0.5833 Remote Similarity NPC23084
0.5833 Remote Similarity NPC479031
0.5818 Remote Similarity NPC294470
0.569 Remote Similarity NPC221090
0.569 Remote Similarity NPC80098
0.5616 Remote Similarity NPC93924
0.5593 Remote Similarity NPC48863
0.5593 Remote Similarity NPC251981
0.5593 Remote Similarity NPC13745
0.5574 Remote Similarity NPC270849
0.5536 Remote Similarity NPC192810
0.5522 Remote Similarity NPC210192
0.5517 Remote Similarity NPC200092
0.5507 Remote Similarity NPC108674
0.5469 Remote Similarity NPC220560
0.5424 Remote Similarity NPC69513
0.5345 Remote Similarity NPC299144
0.5333 Remote Similarity NPC166040
0.5323 Remote Similarity NPC604356
0.5312 Remote Similarity NPC290069
0.5312 Remote Similarity NPC104167
0.5303 Remote Similarity NPC294166
0.5303 Remote Similarity NPC115022
0.5294 Remote Similarity NPC475096
0.5283 Remote Similarity NPC228907
0.5254 Remote Similarity NPC226712
0.5254 Remote Similarity NPC608788
0.5246 Remote Similarity NPC310661
0.5246 Remote Similarity NPC215833
0.5246 Remote Similarity NPC9912
0.5238 Remote Similarity NPC26653
0.5238 Remote Similarity NPC26080
0.5238 Remote Similarity NPC80600
0.5238 Remote Similarity NPC165686
0.5231 Remote Similarity NPC34456
0.5217 Remote Similarity NPC99233
0.5211 Remote Similarity NPC76128
0.5179 Remote Similarity NPC142319
0.5172 Remote Similarity NPC152722
0.5167 Remote Similarity NPC145900
0.5161 Remote Similarity NPC49074
0.5156 Remote Similarity NPC248355
0.5156 Remote Similarity NPC479029
0.5147 Remote Similarity NPC604892
0.5139 Remote Similarity NPC219163
0.5139 Remote Similarity NPC486379
0.5135 Remote Similarity NPC300537
0.5082 Remote Similarity NPC610709
0.5079 Remote Similarity NPC251102
0.5079 Remote Similarity NPC210298
0.5079 Remote Similarity NPC19470
0.5072 Remote Similarity NPC175275
0.5072 Remote Similarity NPC189115
0.507 Remote Similarity NPC271479
0.507 Remote Similarity NPC604833
0.5068 Remote Similarity NPC48640
0.5068 Remote Similarity NPC106625

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC165302 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
0.5254 Remote Similarity NPD1091 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