Natural Product: NPC119336

Natural Product IDNPC119336
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 APHZSLWUGSUBKQ-VBTGVMJWSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 21579142
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000238] Tannins
        • [CHEMONTID:0001710] Hydrolyzable tannins

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 APHZSLWUGSUBKQ-VBTGVMJWSA-N
Standard InCHI InChI=1S/C16H22O10/c1-22-8-4-7(15(21)24-3)5-9(23-2)14(8)26-16-13(20)12(19)11(18)10(6-17)25-16/h4-5,10-13,16-20H,6H2,1-3H3/t10-,11-,12+,13-,16+/m1/s1
SMILES COc1cc(cc(c1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)OC)C(=O)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   374.12 Volume:   345.536
?
Van der Waals volume.
Dense:   1.083 LogP:   -0.457
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.118
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.418
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   13.0
TPSA:   144.14
?
Topological Polar Surface Area.
 H-Bond Acceptor:   10.0
H-Bond Donor:   4.0 Rings:   2.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.442 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.472 Fsp3:   0.562
MCE-18:   54.4
?
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:   0.423 Fluc inhibitor:   0.001
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.095
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.113
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.243 Promiscuous compounds:   0.335

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.468 MDCK Permeability:   -4.853
Pgp-inhibitor:   0.021 Pgp-substrate:   0.195
PAMPA:   0.687
?
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):   0.366
20% Bioavailability (F20%):   0.168 30% Bioavailability (F30%):   0.784
50% Bioavailability (F50%):   0.854

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.444 MRP1:   0.329
Plasma Protein Binding (PPB):   77.658% Volume Distribution (VD):   -0.204
Fu: 22.701%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.996
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.072
BSEP inhibitor:   0.026

ADMET: Metabolism

CYP1A2-inhibitor:   0.011 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.107 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.001 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.003 CYP2D6-substrate:   0.414
CYP3A4-inhibitor:   0.119 CYP3A4-substrate:   0.004
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.982
HLM stability:   0.942
?
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):  2.959 Half-life (T1/2):  3.115

ADMET: Toxicity

hERG Blockers:  0.024 hERG Blockers (10um):  0.147
Human Hepatotoxicity (H-HT):  0.454 Drug-induced Liver Injury (DILI):  0.882
AMES Toxicity:  0.77 Rat Oral Acute Toxicity:  0.024
Maximum Recommended Daily Dose:  0.039 Skin Sensitization:  0.97
Carcinogencity:  0.325 Eye Corrosion:  0.0
Eye Irritation:  0.198 Respiratory Toxicity:  0.011
Drug-induced Neurotoxicity:  0.054 Ototoxicity:  0.898
Hematotoxicity:  0.246 Drug-induced Nephrotoxicity:  0.622
Genotoxicity:  0.217 RPMI-8226 Immunitoxicity:  0.121
A549 Cytotoxicity:  0.089 Hek293 Cytotoxicity:  0.132
BCF:   0.287
?
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:   2.871
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.276
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.616
?
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
NPO4626 Pimpinella anisum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[36432786]
NPO4626 Pimpinella anisum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[36840093]
NPO4626 Pimpinella anisum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[37379658]
NPO4626 Pimpinella anisum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[37446712]
NPO4626 Pimpinella anisum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4626 Pimpinella anisum Species Apiaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO4626 Pimpinella anisum Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO4626 Pimpinella anisum Species Apiaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO4626 Pimpinella anisum Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4626 Pimpinella anisum Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4626 Pimpinella anisum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11302 Hymenidium lindleyanum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4626 Pimpinella anisum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4626 Pimpinella anisum 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 NPC119336 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
0.7347 Intermediate Similarity NPC299144
0.7059 Intermediate Similarity NPC69513
0.7 Intermediate Similarity NPC609376
0.6923 Remote Similarity NPC48863
0.6923 Remote Similarity NPC251981
0.6923 Remote Similarity NPC13745
0.6792 Remote Similarity NPC310661
0.6792 Remote Similarity NPC215833
0.6735 Remote Similarity NPC217854
0.6727 Remote Similarity NPC210478
0.6667 Remote Similarity NPC49074
0.6545 Remote Similarity NPC162093
0.6471 Remote Similarity NPC152722
0.6316 Remote Similarity NPC105827
0.6207 Remote Similarity NPC95392
0.6207 Remote Similarity NPC84013
0.6207 Remote Similarity NPC55715
0.6207 Remote Similarity NPC35877
0.62 Remote Similarity NPC276195
0.6102 Remote Similarity NPC232673
0.6042 Remote Similarity NPC228907
0.6034 Remote Similarity NPC479029
0.6 Remote Similarity NPC166040
0.6 Remote Similarity NPC470236
0.6 Remote Similarity NPC95292
0.5962 Remote Similarity NPC153149
0.5926 Remote Similarity NPC608788
0.5849 Remote Similarity NPC25817
0.5818 Remote Similarity NPC80098
0.5806 Remote Similarity NPC479030
0.5789 Remote Similarity NPC218685
0.5781 Remote Similarity NPC216129
0.5781 Remote Similarity NPC130449
0.5781 Remote Similarity NPC248132
0.569 Remote Similarity NPC472024
0.569 Remote Similarity NPC270849
0.5636 Remote Similarity NPC226712
0.5593 Remote Similarity NPC26653
0.5593 Remote Similarity NPC80600
0.5577 Remote Similarity NPC212729
0.5577 Remote Similarity NPC604498
0.5536 Remote Similarity NPC145900
0.5526 Remote Similarity NPC470685
0.5526 Remote Similarity NPC485744
0.55 Remote Similarity NPC248355
0.5472 Remote Similarity NPC269242
0.5469 Remote Similarity NPC146803
0.5455 Remote Similarity NPC479447
0.5424 Remote Similarity NPC479028
0.5424 Remote Similarity NPC23084
0.5424 Remote Similarity NPC479031
0.5424 Remote Similarity NPC606892
0.541 Remote Similarity NPC55040
0.541 Remote Similarity NPC599943
0.5385 Remote Similarity NPC475096
0.5385 Remote Similarity NPC475084
0.5373 Remote Similarity NPC604833
0.537 Remote Similarity NPC192810
0.537 Remote Similarity NPC294470
0.5345 Remote Similarity NPC40377
0.5345 Remote Similarity NPC9912
0.5333 Remote Similarity NPC164599
0.5323 Remote Similarity NPC302378
0.5323 Remote Similarity NPC609355
0.5312 Remote Similarity NPC486107
0.5283 Remote Similarity NPC142319
0.5263 Remote Similarity NPC221090
0.5246 Remote Similarity NPC609351
0.5238 Remote Similarity NPC603686
0.5231 Remote Similarity NPC164857
0.5231 Remote Similarity NPC604892
0.5224 Remote Similarity NPC478798
0.5217 Remote Similarity NPC51328
0.5217 Remote Similarity NPC55158
0.5179 Remote Similarity NPC60589
0.5179 Remote Similarity NPC469708
0.5179 Remote Similarity NPC190730
0.5179 Remote Similarity NPC604439
0.5161 Remote Similarity NPC104167
0.5156 Remote Similarity NPC276753
0.5156 Remote Similarity NPC205796
0.5152 Remote Similarity NPC210192
0.5147 Remote Similarity NPC299435
0.5139 Remote Similarity NPC605526
0.5088 Remote Similarity NPC200092
0.5088 Remote Similarity NPC12308
0.5079 Remote Similarity NPC247146
0.5079 Remote Similarity NPC34456
0.5079 Remote Similarity NPC607971
0.5077 Remote Similarity NPC37468
0.5077 Remote Similarity NPC246947
0.5077 Remote Similarity NPC604095
0.5075 Remote Similarity NPC485147
0.5072 Remote Similarity NPC191046
0.507 Remote Similarity NPC199539

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC119336 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
0.5636 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