Natural Product: NPC24681

Natural Product IDNPC24681
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 BUJOWQKLLDUNTC-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 441782
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000301] Benzofurans
        • [CHEMONTID:0000015] Dibenzofurans

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 BUJOWQKLLDUNTC-UHFFFAOYSA-N
Standard InCHI InChI=1S/C15H14O6/c1-18-12-6-11-7(4-9(12)16)8-5-10(17)14(19-2)15(20-3)13(8)21-11/h4-6,16-17H,1-3H3
SMILES COc1cc2c(cc1O)c1cc(c(c(c1o2)OC)OC)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   290.08 Volume:   279.249
?
Van der Waals volume.
Dense:   1.039 LogP:   2.256
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.465
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.483
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   15.0
TPSA:   81.29
?
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:   0.771 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.476 Fsp3:   0.2
MCE-18:   18.0
?
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:   1 PAINS Alert:   0
Colloidal aggregators:   0.441 Fluc inhibitor:   0.384
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.899
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.51
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.383 Promiscuous compounds:   0.629

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.174 MDCK Permeability:   -4.765
Pgp-inhibitor:   0.004 Pgp-substrate:   0.288
PAMPA:   0.558
?
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):   0.135
20% Bioavailability (F20%):   0.625 30% Bioavailability (F30%):   0.607
50% Bioavailability (F50%):   0.982

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.009 MRP1:   0.953
Plasma Protein Binding (PPB):   86.628% Volume Distribution (VD):   -0.492
Fu: 12.082%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.974
OATP1B3 inhibitor:   0.997 BCRP inhibitor:   0.789
BSEP inhibitor:   0.554

ADMET: Metabolism

CYP1A2-inhibitor:   0.398 CYP1A2-substrate:   0.986
CYP2C19-inhibitor:   0.018 CYP2C19-substrate:   0.683
CYP2C9-inhibitor:   0.2 CYP2C9-substrate:   0.738
CYP2D6-inhibitor:   0.81 CYP2D6-substrate:   0.496
CYP3A4-inhibitor:   0.873 CYP3A4-substrate:   0.999
CYP2B6-substrate:   0.016 CYP2C8-inhibitor:   1.0
HLM stability:   0.408
?
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):  5.198 Half-life (T1/2):  1.741

ADMET: Toxicity

hERG Blockers:  0.091 hERG Blockers (10um):  0.57
Human Hepatotoxicity (H-HT):  0.449 Drug-induced Liver Injury (DILI):  0.631
AMES Toxicity:  0.49 Rat Oral Acute Toxicity:  0.449
Maximum Recommended Daily Dose:  0.497 Skin Sensitization:  0.732
Carcinogencity:  0.745 Eye Corrosion:  0.527
Eye Irritation:  0.985 Respiratory Toxicity:  0.799
Drug-induced Neurotoxicity:  0.212 Ototoxicity:  0.176
Hematotoxicity:  0.256 Drug-induced Nephrotoxicity:  0.139
Genotoxicity:  0.151 RPMI-8226 Immunitoxicity:  0.121
A549 Cytotoxicity:  0.244 Hek293 Cytotoxicity:  0.4
BCF:   1.356
?
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:   3.958
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.522
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.976
?
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
NPO22761 Gentiana cruciata Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)88887-1]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. DOI[10.1071/CH03175]
NPO14117 Diplodia sapinea Species Botryosphaeriaceae Eukaryota n.a. n.a. n.a. PMID[10075753]
NPO24512 Xestospongia testudinaria Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[10543913]
NPO25046 Aplidium meridianum Species Polyclinidae Eukaryota n.a. South Georgia Islands, South Atlantic n.a. PMID[15026054]
NPO20590 Justicia patentiflora Species Acanthaceae Eukaryota n.a. Vietnamese n.a. PMID[15921419]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO25391 Vitex glabrata Species Lamiaceae Eukaryota leaves Chantaburi Province, Thailand 2007-Nov PMID[19943620]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota twigs n.a. n.a. PMID[20058933]
NPO21423 Botryllus tuberatus Species Styelidae Eukaryota n.a. Korean n.a. PMID[21142112]
NPO21423 Botryllus tuberatus Species Styelidae Eukaryota n.a. n.a. n.a. PMID[21142112]
NPO28887 Eupomatia laurina Species Eupomatiaceae Eukaryota n.a. n.a. n.a. PMID[21504145]
NPO24745 Salvia cavaleriei Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[24256484]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota flowers Pakook, Muang District, Chiang Rai Province, Thailand 2013-Feb PMID[25651042]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota young fruits Khokkhon, Tha Bo District, Nong Khai Province, Thailand 2011-Aug PMID[25651042]
NPO25416 Uncaria cordata Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[27128898]
NPO22780 Sphaeranthus africanus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[30074787]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota Leaves n.a. n.a. PMID[31860303]
NPO25046 Aplidium meridianum Species Polyclinidae Eukaryota n.a. n.a. n.a. PMID[9748381]
NPO24601 Rumex dentatus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18812 Vicia narbonensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27436 Ribes uva-crispa Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25700 Psiadia punctulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28887 Eupomatia laurina Species Eupomatiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25625 Hymenophyllum recurvum Species Hymenophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13767 Woodfordia fruticosa Species Lythraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25391 Vitex glabrata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25416 Uncaria cordata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22780 Sphaeranthus africanus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24512 Xestospongia testudinaria Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13588 Sanguinaria canadensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20590 Justicia patentiflora Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25091 Samadera bidwillii Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24745 Salvia cavaleriei Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5027 Peniophora polygonia Species Peniophoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23568 Guatteria pogonopus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18842 Gnaphalium gaudichaudianum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22761 Gentiana cruciata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14117 Diplodia sapinea Species Botryosphaeriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25364 Didemnum candidum Species Didemnidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22293 Bryobium hyacinthoides Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24077 Astragalus pterocarpus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25046 Aplidium meridianum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO27436 Ribes uva-crispa Species n.a. n.a. Fruits n.a. Database[FooDB]
NPO27436 Ribes uva-crispa Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO27436 Ribes uva-crispa Species n.a. n.a. Fruit n.a. n.a. Database[FooDB]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO25416 Uncaria cordata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13767 Woodfordia fruticosa Species Lythraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24077 Astragalus pterocarpus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24601 Rumex dentatus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13588 Sanguinaria canadensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO24601 Rumex dentatus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13588 Sanguinaria canadensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13767 Woodfordia fruticosa Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25416 Uncaria cordata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24077 Astragalus pterocarpus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24601 Rumex dentatus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20335 Nassauvia pygmaea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24077 Astragalus pterocarpus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13767 Woodfordia fruticosa Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22780 Sphaeranthus africanus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14117 Diplodia sapinea Species Botryosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28887 Eupomatia laurina Species Eupomatiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13588 Sanguinaria canadensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18842 Gnaphalium gaudichaudianum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25625 Hymenophyllum recurvum Species Hymenophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27436 Ribes uva-crispa Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO18812 Vicia narbonensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22761 Gentiana cruciata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22293 Bryobium hyacinthoides Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20590 Justicia patentiflora Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24512 Xestospongia testudinaria Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25046 Aplidium meridianum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5027 Peniophora polygonia Species Peniophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25091 Samadera bidwillii Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25700 Psiadia punctulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24745 Salvia cavaleriei Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23568 Guatteria pogonopus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25416 Uncaria cordata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25364 Didemnum candidum Species Didemnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24601 Rumex dentatus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21423 Botryllus tuberatus Species Styelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25391 Vitex glabrata Species Lamiaceae 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 NPC24681 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
0.6522 Remote Similarity NPC39305
0.6042 Remote Similarity NPC238995
0.5833 Remote Similarity NPC59295
0.5745 Remote Similarity NPC45449

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC24681 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