Natural Product: NPC141357

Natural Product IDNPC141357
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 CGQIQSHSLSNQMC-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 21270126
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0002901] Isoflav-2-enes
          • [CHEMONTID:0000494] Isoflavones

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 CGQIQSHSLSNQMC-UHFFFAOYSA-N
Standard InCHI InChI=1S/C16H10O5/c17-10-3-1-9(2-4-10)12-7-19-13-6-15-14(20-8-21-15)5-11(13)16(12)18/h1-7,17H,8H2
SMILES c1cc(ccc1c1coc2cc3c(cc2c1=O)OCO3)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   282.05 Volume:   273.926
?
Van der Waals volume.
Dense:   1.03 LogP:   2.509
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.537
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.255
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   22.0
TPSA:   68.9
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   1.0 Rings:   4.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.743 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.25 Fsp3:   0.062
MCE-18:   42.353
?
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:   0.607 Fluc inhibitor:   0.996
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.975
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.535
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.469 Promiscuous compounds:   0.403

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.822 MDCK Permeability:   -4.723
Pgp-inhibitor:   0.078 Pgp-substrate:   0.052
PAMPA:   0.868
?
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):   0.02
20% Bioavailability (F20%):   0.331 30% Bioavailability (F30%):   0.117
50% Bioavailability (F50%):   0.643

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.116 MRP1:   0.426
Plasma Protein Binding (PPB):   90.72% Volume Distribution (VD):   0.032
Fu: 10.519%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.692
OATP1B3 inhibitor:   0.7 BCRP inhibitor:   0.286
BSEP inhibitor:   0.954

ADMET: Metabolism

CYP1A2-inhibitor:   0.977 CYP1A2-substrate:   0.995
CYP2C19-inhibitor:   0.014 CYP2C19-substrate:   0.976
CYP2C9-inhibitor:   0.947 CYP2C9-substrate:   0.999
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.916
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.999
CYP2B6-substrate:   0.101 CYP2C8-inhibitor:   0.705
HLM stability:   0.001
?
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):  5.523 Half-life (T1/2):  0.941

ADMET: Toxicity

hERG Blockers:  0.22 hERG Blockers (10um):  0.573
Human Hepatotoxicity (H-HT):  0.528 Drug-induced Liver Injury (DILI):  0.719
AMES Toxicity:  0.575 Rat Oral Acute Toxicity:  0.556
Maximum Recommended Daily Dose:  0.738 Skin Sensitization:  0.333
Carcinogencity:  0.866 Eye Corrosion:  0.132
Eye Irritation:  0.973 Respiratory Toxicity:  0.633
Drug-induced Neurotoxicity:  0.603 Ototoxicity:  0.225
Hematotoxicity:  0.22 Drug-induced Nephrotoxicity:  0.261
Genotoxicity:  0.869 RPMI-8226 Immunitoxicity:  0.073
A549 Cytotoxicity:  0.181 Hek293 Cytotoxicity:  0.569
BCF:   1.306
?
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:   3.85
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.92
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.403
?
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
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[11599360]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. seed n.a. PMID[21381697]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[37120447]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7639 Senecio isatideus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14100 Persea kusanoi Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO433 Geranium sibiricum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2263 Croton megistocarpus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8075 Cacospongia scalaris Species Thorectidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO433 Geranium sibiricum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO433 Geranium sibiricum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO433 Geranium sibiricum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7639 Senecio isatideus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8075 Cacospongia scalaris Species Thorectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8210 Trigonella foenum-graecum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2263 Croton megistocarpus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14100 Persea kusanoi Species Lauraceae 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 NPC141357 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 NPC605229
0.7069 Intermediate Similarity NPC285973
0.6833 Remote Similarity NPC62518
0.6379 Remote Similarity NPC181124
0.6379 Remote Similarity NPC100971
0.6271 Remote Similarity NPC148497
0.6102 Remote Similarity NPC216769
0.5873 Remote Similarity NPC35544
0.5789 Remote Similarity NPC120924
0.5775 Remote Similarity NPC259070
0.5714 Remote Similarity NPC234560
0.5694 Remote Similarity NPC105511
0.5692 Remote Similarity NPC260640
0.5614 Remote Similarity NPC218490
0.5574 Remote Similarity NPC162680
0.5574 Remote Similarity NPC303644
0.5484 Remote Similarity NPC279061
0.5484 Remote Similarity NPC487217
0.5469 Remote Similarity NPC603384
0.5424 Remote Similarity NPC195919
0.541 Remote Similarity NPC7013
0.541 Remote Similarity NPC269451
0.5345 Remote Similarity NPC125449
0.5323 Remote Similarity NPC186507
0.5312 Remote Similarity NPC602183
0.5217 Remote Similarity NPC168085
0.5161 Remote Similarity NPC603503
0.5156 Remote Similarity NPC52623
0.5152 Remote Similarity NPC104728
0.5135 Remote Similarity NPC211014
0.5085 Remote Similarity NPC39426
0.5079 Remote Similarity NPC121522
0.5079 Remote Similarity NPC209560
0.5079 Remote Similarity NPC490700
0.5077 Remote Similarity NPC220050
0.5075 Remote Similarity NPC225624
0.5067 Remote Similarity NPC161749

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC141357 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
0.5085 Remote Similarity NPD1510 Phase 2
0.5067 Remote Similarity NPD4381 Clinical (unspecified phase)

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