Natural Product: NPC302260

Natural Product IDNPC302260
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 BGMOXLYBBTWIMD-CRCLSJGQSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10986239
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001983] Dihydrofurans
        • [CHEMONTID:0001982] Furanones
          • [CHEMONTID:0002223] Butenolides

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 BGMOXLYBBTWIMD-CRCLSJGQSA-N
Standard InCHI InChI=1S/C6H8O3/c1-4(7)5-2-3-6(8)9-5/h2-5,7H,1H3/t4-,5+/m0/s1
SMILES C[C@@H]([C@H]1C=CC(=O)O1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   128.05 Volume:   124.874
?
Van der Waals volume.
Dense:   1.025 LogP:   -0.03
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.051
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.348
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   6.0
TPSA:   46.53
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   1.0 Rings:   1.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.499 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.929 Fsp3:   0.5
MCE-18:   13.333
?
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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.391 Fluc inhibitor:   0.303
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.147
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.003
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.88 Promiscuous compounds:   0.685

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.87 MDCK Permeability:   -4.625
Pgp-inhibitor:   0.094 Pgp-substrate:   0.136
PAMPA:   0.791
?
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):   0.528
20% Bioavailability (F20%):   0.483 30% Bioavailability (F30%):   0.684
50% Bioavailability (F50%):   0.554

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.206 MRP1:   0.506
Plasma Protein Binding (PPB):   8.645% Volume Distribution (VD):   -0.175
Fu: 92.003%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.753
OATP1B3 inhibitor:   0.933 BCRP inhibitor:   0.022
BSEP inhibitor:   0.557

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.018
CYP2C19-inhibitor:   0.051 CYP2C19-substrate:   0.005
CYP2C9-inhibitor:   0.015 CYP2C9-substrate:   0.055
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.003
CYP3A4-inhibitor:   0.002 CYP3A4-substrate:   0.724
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.969
HLM stability:   0.733
?
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):  3.426 Half-life (T1/2):  2.735

ADMET: Toxicity

hERG Blockers:  0.022 hERG Blockers (10um):  0.323
Human Hepatotoxicity (H-HT):  0.373 Drug-induced Liver Injury (DILI):  0.27
AMES Toxicity:  0.55 Rat Oral Acute Toxicity:  0.519
Maximum Recommended Daily Dose:  0.094 Skin Sensitization:  0.987
Carcinogencity:  0.382 Eye Corrosion:  0.995
Eye Irritation:  0.997 Respiratory Toxicity:  0.149
Drug-induced Neurotoxicity:  0.421 Ototoxicity:  0.194
Hematotoxicity:  0.332 Drug-induced Nephrotoxicity:  0.382
Genotoxicity:  0.253 RPMI-8226 Immunitoxicity:  0.052
A549 Cytotoxicity:  0.084 Hek293 Cytotoxicity:  0.048
BCF:   0.29
?
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:   2.875
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.914
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.413
?
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
NPO29205 Vepris fitoravina Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24755 Abies nordmanniana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28886 Acacia latifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18494 Carassea connexa Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29451 Clostridium tertium Species Clostridiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO28972 Comatula solaris Species Comatulidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28846 Doris nobilis Species Dorididae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22014 Dysphania botrys Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29489 Garcinia opaca Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28866 Haematomma ochrophaeum Species Haematommataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29173 Leucadendron adscendens Species Proteaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28951 Manglietia phuthoensis Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29029 Ophistreptus levis n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO29128 Pimpinella heyneana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28900 Planobispora rosea Species Streptosporangiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO29416 Rhodophyllus nidorosus Species Entolomataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18062 Tapinella atrotomentosa Species Tapinellaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29532 Vigna angularis Species Fabaceae Eukaryota Leaf Diffusate n.a. n.a. Database[FooDB]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29532 Vigna angularis Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29532 Vigna angularis Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO22014 Dysphania botrys Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29451 Clostridium tertium Species Clostridiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO28972 Comatula solaris Species Comatulidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29205 Vepris fitoravina Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28846 Doris nobilis Species Dorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18494 Carassea connexa Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28886 Acacia latifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24755 Abies nordmanniana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28866 Haematomma ochrophaeum Species Haematommataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28900 Planobispora rosea Species Streptosporangiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO29128 Pimpinella heyneana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29416 Rhodophyllus nidorosus Species Entolomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29173 Leucadendron adscendens Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28951 Manglietia phuthoensis Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29489 Garcinia opaca Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22014 Dysphania botrys Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29029 Ophistreptus levis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO18062 Tapinella atrotomentosa Species Tapinellaceae 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 NPC302260 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
0.6207 Remote Similarity NPC276299
0.6071 Remote Similarity NPC302564

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC302260 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