Natural Product: NPC305766

Natural Product IDNPC305766
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 AQDIJIAUYXOCGX-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 76600
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0000176] Benzoic acids and derivatives
          • [CHEMONTID:0001248] Hydroxybenzoic acid derivatives

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 AQDIJIAUYXOCGX-UHFFFAOYSA-N
Standard InCHI InChI=1S/C8H8O5/c1-13-8(12)7-5(10)2-4(9)3-6(7)11/h2-3,9-11H,1H3
SMILES COC(=O)c1c(cc(cc1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   184.04 Volume:   171.773
?
Van der Waals volume.
Dense:   1.071 LogP:   1.258
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.501
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.077
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   7.0
TPSA:   86.99
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   3.0 Rings:   1.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.556 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.178 Fsp3:   0.125
MCE-18:   8.0
?
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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.361 Fluc inhibitor:   0.004
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.097
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.006
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.988 Promiscuous compounds:   0.977

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.428 MDCK Permeability:   -4.92
Pgp-inhibitor:   0.023 Pgp-substrate:   0.067
PAMPA:   0.33
?
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):   0.002
20% Bioavailability (F20%):   0.029 30% Bioavailability (F30%):   0.427
50% Bioavailability (F50%):   0.866

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.124 MRP1:   0.954
Plasma Protein Binding (PPB):   91.726% Volume Distribution (VD):   -0.308
Fu: 8.434%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.937
OATP1B3 inhibitor:   0.997 BCRP inhibitor:   0.583
BSEP inhibitor:   0.118

ADMET: Metabolism

CYP1A2-inhibitor:   0.957 CYP1A2-substrate:   0.582
CYP2C19-inhibitor:   0.02 CYP2C19-substrate:   0.131
CYP2C9-inhibitor:   0.983 CYP2C9-substrate:   0.854
CYP2D6-inhibitor:   0.996 CYP2D6-substrate:   0.892
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.386
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.46
HLM stability:   0.687
?
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):  8.483 Half-life (T1/2):  0.902

ADMET: Toxicity

hERG Blockers:  0.03 hERG Blockers (10um):  0.579
Human Hepatotoxicity (H-HT):  0.122 Drug-induced Liver Injury (DILI):  0.258
AMES Toxicity:  0.372 Rat Oral Acute Toxicity:  0.259
Maximum Recommended Daily Dose:  0.388 Skin Sensitization:  0.695
Carcinogencity:  0.434 Eye Corrosion:  0.37
Eye Irritation:  0.998 Respiratory Toxicity:  0.745
Drug-induced Neurotoxicity:  0.105 Ototoxicity:  0.107
Hematotoxicity:  0.026 Drug-induced Nephrotoxicity:  0.05
Genotoxicity:  0.471 RPMI-8226 Immunitoxicity:  0.066
A549 Cytotoxicity:  0.184 Hek293 Cytotoxicity:  0.488
BCF:   0.966
?
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:   3.425
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.406
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.708
?
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
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2004.07.004]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota Whole plant n.a. n.a. PMID[11141121]
NPO16999 Paeonia emodi Species Paeoniaceae Eukaryota n.a. root n.a. PMID[12612406]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[17011103]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO14827 Rhus chinensis Species Anacardiaceae Eukaryota Roots n.a. n.a. PMID[32031812]
NPO10580 Herba glechomae n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6890 Euphorbia jolkinii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18641 Radix euphorbiae pekinensis Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24267 Paeonia veitchii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9602 Rosa multiflora Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21458 Radix paeoniae rubra Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11673 Koelreuteria paniculata Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27520 Casuarina equisetifolia Species Casuarinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16999 Paeonia emodi Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota Roots n.a. Database[FooDB]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9602 Rosa multiflora Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1775 Euphorbia pekinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27520 Casuarina equisetifolia Species Casuarinaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16999 Paeonia emodi Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11673 Koelreuteria paniculata Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24267 Paeonia veitchii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14827 Rhus chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO14827 Rhus chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1775 Euphorbia pekinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11673 Koelreuteria paniculata Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10580 Herba glechomae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO24267 Paeonia veitchii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18641 Radix euphorbiae pekinensis Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6890 Euphorbia jolkinii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16999 Paeonia emodi Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21458 Radix paeoniae rubra Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27520 Casuarina equisetifolia Species Casuarinaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9602 Rosa multiflora Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23740 Jacobaea analoga Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14827 Rhus chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24267 Paeonia veitchii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9602 Rosa multiflora Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1775 Euphorbia pekinensis Species Euphorbiaceae 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]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27520 Casuarina equisetifolia Species Casuarinaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11673 Koelreuteria paniculata Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1775 Euphorbia pekinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9602 Rosa multiflora Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14827 Rhus chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4593 Lagerstroemia indica Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9602 Rosa multiflora Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16999 Paeonia emodi Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27520 Casuarina equisetifolia Species Casuarinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11673 Koelreuteria paniculata Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1775 Euphorbia pekinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24559 Cotinus coggygria Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24267 Paeonia veitchii Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14827 Rhus chinensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6890 Euphorbia jolkinii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23740 Jacobaea analoga 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 NPC305766 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
0.6429 Remote Similarity NPC607792
0.6 Remote Similarity NPC95309
0.5806 Remote Similarity NPC189823
0.5185 Remote Similarity NPC230349

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC305766 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