Natural Product: NPC254057

Natural Product IDNPC254057
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 LGXRGPOUGZXSEB-NSHDSACASA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 169739
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000027] Indanes
        • [CHEMONTID:0001151] Indanones

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 LGXRGPOUGZXSEB-NSHDSACASA-N
Standard InCHI InChI=1S/C14H18O3/c1-8-5-10-6-11(7-16)14(17)13(10)9(2)12(8)3-4-15/h5,11,15-16H,3-4,6-7H2,1-2H3/t11-/m0/s1
SMILES Cc1cc2C[C@@H](CO)C(=O)c2c(C)c1CCO

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   234.13 Volume:   249.412
?
Van der Waals volume.
Dense:   0.939 LogP:   1.691
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.847
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.598
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   11.0
TPSA:   57.53
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   2.0 Rings:   2.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.826 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.268 Fsp3:   0.5
MCE-18:   41.476
?
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:   0.015 Fluc inhibitor:   0.317
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.473
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.062
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.317 Promiscuous compounds:   0.475

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.872 MDCK Permeability:   -4.682
Pgp-inhibitor:   0.343 Pgp-substrate:   0.672
PAMPA:   0.783
?
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):   0.003
20% Bioavailability (F20%):   0.056 30% Bioavailability (F30%):   0.143
50% Bioavailability (F50%):   0.721

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.07 MRP1:   0.95
Plasma Protein Binding (PPB):   70.99% Volume Distribution (VD):   0.186
Fu: 25.664%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.798
OATP1B3 inhibitor:   0.857 BCRP inhibitor:   0.028
BSEP inhibitor:   0.953

ADMET: Metabolism

CYP1A2-inhibitor:   0.881 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.3 CYP2C19-substrate:   0.003
CYP2C9-inhibitor:   0.855 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.563 CYP2D6-substrate:   0.273
CYP3A4-inhibitor:   0.927 CYP3A4-substrate:   0.15
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.086
HLM stability:   0.095
?
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):  6.725 Half-life (T1/2):  1.693

ADMET: Toxicity

hERG Blockers:  0.051 hERG Blockers (10um):  0.138
Human Hepatotoxicity (H-HT):  0.676 Drug-induced Liver Injury (DILI):  0.687
AMES Toxicity:  0.816 Rat Oral Acute Toxicity:  0.175
Maximum Recommended Daily Dose:  0.086 Skin Sensitization:  0.994
Carcinogencity:  0.682 Eye Corrosion:  0.098
Eye Irritation:  0.963 Respiratory Toxicity:  0.61
Drug-induced Neurotoxicity:  0.556 Ototoxicity:  0.812
Hematotoxicity:  0.722 Drug-induced Nephrotoxicity:  0.786
Genotoxicity:  0.213 RPMI-8226 Immunitoxicity:  0.108
A549 Cytotoxicity:  0.26 Hek293 Cytotoxicity:  0.204
BCF:   0.618
?
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:   3.208
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.485
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.784
?
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
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. DOI[10.1039/C39770000295]
NPO7574 Garcinia pyrifera Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[10978200]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. PMID[11032480]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[11429258]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota stem bark Medicinal Plant Garden, College of Pharmacy, Ewha Womans University 2013-DEC PMID[28787158]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. stem n.a. PMID[8945767]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[9599262]
NPO11531 Duguetia calycina Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12411 Eriostemon spicatus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10861 Dipsacus asper Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13121 Crepidiastrum sonchifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11032 Coutarea latifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1776 Attalea excelsa Species Arecaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2593 Coccolithus huxleyi Species Coccolithaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12516 Phalaris canariensis Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16247 Talaromyces bacillisporus Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7705 Navanax inermis Species Aglajidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27659 Tanacetum parthenifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12030 Streptomyces yokosukanensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11214 Rivina humilis Species Petiveriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7313 Epirrhoe sperryi Species Geometridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12971 Payena lucida Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8389 Ophryosporus floribundus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12858 Jacaranda chelonia Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5727 Hymenothrix wislizenii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO716 Greenwayodendron oliveri Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7574 Garcinia pyrifera Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2384 Ircinia ramosa Species Irciniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6671 Ulva conglobata Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10861 Dipsacus asper Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11531 Duguetia calycina Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27659 Tanacetum parthenifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12030 Streptomyces yokosukanensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16247 Talaromyces bacillisporus Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7313 Epirrhoe sperryi Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12971 Payena lucida Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO716 Greenwayodendron oliveri Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10861 Dipsacus asper Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11032 Coutarea latifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8389 Ophryosporus floribundus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5727 Hymenothrix wislizenii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7705 Navanax inermis Species Aglajidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2384 Ircinia ramosa Species Irciniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17700 Ilex dunniana Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2593 Coccolithus huxleyi Species Coccolithaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12366 Calotis multicaulis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8186 Ocotea minarum Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1776 Attalea excelsa Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12411 Eriostemon spicatus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11214 Rivina humilis Species Petiveriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6671 Ulva conglobata Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13121 Crepidiastrum sonchifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7574 Garcinia pyrifera Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12858 Jacaranda chelonia Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12516 Phalaris canariensis Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6938 Astragalus dissectus Species Fabaceae 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 NPC254057 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
0.7692 Intermediate Similarity NPC83409
0.5556 Remote Similarity NPC112903
0.5435 Remote Similarity NPC135654
0.5435 Remote Similarity NPC190729

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC254057 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
NPD

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