Natural Product: NPC42051

Natural Product IDNPC42051
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 NVUHVZUPJHEJGT-CWDCEQMOSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 24761001
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000301] Benzofurans
        • [CHEMONTID:0001578] Benzofuranones

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 NVUHVZUPJHEJGT-CWDCEQMOSA-N
Standard InCHI InChI=1S/C17H15NO5/c1-3-4-9-5-13(20)12(8-18-9)16-15-11(17(21)23-16)6-10(19)7-14(15)22-2/h3-8,16,19H,1-2H3,(H,18,20)/b4-3+/t16-/m0/s1
SMILES C/C=C/c1cc(=O)c(c[nH]1)[C@H]1c2c(cc(cc2OC)O)C(=O)O1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   313.1 Volume:   310.775
?
Van der Waals volume.
Dense:   1.007 LogP:   1.319
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.602
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.722
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   19.0
TPSA:   88.62
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   2.0 Rings:   3.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.849 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.65 Fsp3:   0.176
MCE-18:   55.8
?
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:   0.456 Fluc inhibitor:   0.622
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.285
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.379
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.108 Promiscuous compounds:   0.423

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.12 MDCK Permeability:   -4.879
Pgp-inhibitor:   0.012 Pgp-substrate:   0.789
PAMPA:   0.018
?
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):   0.0
20% Bioavailability (F20%):   0.144 30% Bioavailability (F30%):   0.195
50% Bioavailability (F50%):   0.897

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.015 MRP1:   0.894
Plasma Protein Binding (PPB):   97.583% Volume Distribution (VD):   -0.107
Fu: 2.822%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.322
OATP1B3 inhibitor:   0.222 BCRP inhibitor:   0.415
BSEP inhibitor:   0.965

ADMET: Metabolism

CYP1A2-inhibitor:   0.033 CYP1A2-substrate:   0.95
CYP2C19-inhibitor:   0.007 CYP2C19-substrate:   0.841
CYP2C9-inhibitor:   0.239 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.026 CYP2D6-substrate:   0.796
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   0.119
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.997
HLM stability:   0.976
?
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):  8.07 Half-life (T1/2):  0.984

ADMET: Toxicity

hERG Blockers:  0.061 hERG Blockers (10um):  0.428
Human Hepatotoxicity (H-HT):  0.778 Drug-induced Liver Injury (DILI):  0.971
AMES Toxicity:  0.911 Rat Oral Acute Toxicity:  0.683
Maximum Recommended Daily Dose:  0.985 Skin Sensitization:  0.997
Carcinogencity:  0.92 Eye Corrosion:  0.002
Eye Irritation:  0.771 Respiratory Toxicity:  0.744
Drug-induced Neurotoxicity:  0.968 Ototoxicity:  0.198
Hematotoxicity:  0.36 Drug-induced Nephrotoxicity:  0.975
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.361
A549 Cytotoxicity:  0.608 Hek293 Cytotoxicity:  0.639
BCF:   1.301
?
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:   4.008
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.564
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.922
?
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
NPO18252 Cajanus cajan Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[136119]
NPO16746 Lendenfeldia frondosa Species Thorectidae Eukaryota n.a. n.a. n.a. PMID[1402955]
NPO18252 Cajanus cajan Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO18252 Cajanus cajan Species Fabaceae Eukaryota n.a. leaf n.a. PMID[24680612]
NPO6425 Betula davurica Species Betulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18252 Cajanus cajan Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14953 Thapsia transtagana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15430 Abutilon grandiflorum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29099 Sinocrassula indica Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19229 Aniba parviflora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14711.1 Arabidopsis lyrata subsp. lyrata Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18497 Euphorbia aellenii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13673 Ipomoea muelleri Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11042 Lecanora sordida Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17440 Thryptomene kochii Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18008 Viburnum rhytidophyllum Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18830 Valeriana cardamines Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19073 Uncaria lancifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3022 Toxicopueraria peduncularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16746 Lendenfeldia frondosa Species Thorectidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23370 Sticta mougeotiana Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19692 Quercus variabilis Species Fagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18659 Prunus japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16040 Pristimera indica Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28174 Poterium sanguisorba Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11777 Pluchea sericea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19753 Liabum bourgeaui Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18252 Cajanus cajan Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO18252 Cajanus cajan Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO18252 Cajanus cajan Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16040 Pristimera indica Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18659 Prunus japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19073 Uncaria lancifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18252 Cajanus cajan Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO16040 Pristimera indica Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18659 Prunus japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11777 Pluchea sericea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19073 Uncaria lancifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3022 Toxicopueraria peduncularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18659 Prunus japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18659 Prunus japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29099 Sinocrassula indica Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28174 Poterium sanguisorba Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23370 Sticta mougeotiana Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19073 Uncaria lancifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16040 Pristimera indica Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14711.1 Arabidopsis lyrata subsp. lyrata Subspecies Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18830 Valeriana cardamines Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14953 Thapsia transtagana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18497 Euphorbia aellenii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6425 Betula davurica Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18008 Viburnum rhytidophyllum Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19692 Quercus variabilis Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11042 Lecanora sordida Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18252 Cajanus cajan Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16746 Lendenfeldia frondosa Species Thorectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18659 Prunus japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13673 Ipomoea muelleri Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3022 Toxicopueraria peduncularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19229 Aniba parviflora Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15430 Abutilon grandiflorum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17440 Thryptomene kochii Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19753 Liabum bourgeaui Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11777 Pluchea sericea Species Asteraceae 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 NPC42051 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
NPC

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC42051 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