Natural Product: NPC488674

Natural Product IDNPC488674
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 FECBGSZJXZAMNN-OZOSWLFCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 127026398
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002650] Diarylheptanoids
        • [CHEMONTID:0002652] Cyclic diarylheptanoids
          • [CHEMONTID:0003524] Meta,meta-bridged biphenyls

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 FECBGSZJXZAMNN-OZOSWLFCSA-N
Standard InCHI InChI=1S/C19H22O6/c20-12-5-10-1-3-15(21)13(6-10)14-7-11(2-4-16(14)22)8-17(23)19(25)18(24)9-12/h1-4,6-7,12,17-25H,5,8-9H2/t12-,17-,18-,19+/m0/s1
SMILES c1cc(c2-c3cc(ccc3O)C[C@@H]([C@H]([C@H](C[C@H](Cc1c2)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   346.14 Volume:   348.433
?
Van der Waals volume.
Dense:   0.993 LogP:   0.94
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.346
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.373
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   21.0
TPSA:   121.38
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   6.0 Rings:   3.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.418 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.399 Fsp3:   0.368
MCE-18:   67.231
?
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:   0.565 Fluc inhibitor:   0.019
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.609
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.069
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.421 Promiscuous compounds:   0.241

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.638 MDCK Permeability:   -4.843
Pgp-inhibitor:   0.0 Pgp-substrate:   0.982
PAMPA:   0.999
?
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):   0.017
20% Bioavailability (F20%):   0.773 30% Bioavailability (F30%):   0.882
50% Bioavailability (F50%):   0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.198
Plasma Protein Binding (PPB):   64.78% Volume Distribution (VD):   -0.091
Fu: 35.896%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.98
OATP1B3 inhibitor:   0.994 BCRP inhibitor:   0.025
BSEP inhibitor:   0.164

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.083 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.01
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.242
HLM stability:   0.564
?
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):  8.348 Half-life (T1/2):  3.139

ADMET: Toxicity

hERG Blockers:  0.077 hERG Blockers (10um):  0.361
Human Hepatotoxicity (H-HT):  0.452 Drug-induced Liver Injury (DILI):  0.046
AMES Toxicity:  0.507 Rat Oral Acute Toxicity:  0.092
Maximum Recommended Daily Dose:  0.699 Skin Sensitization:  0.178
Carcinogencity:  0.251 Eye Corrosion:  0.0
Eye Irritation:  0.836 Respiratory Toxicity:  0.141
Drug-induced Neurotoxicity:  0.027 Ototoxicity:  0.939
Hematotoxicity:  0.071 Drug-induced Nephrotoxicity:  0.779
Genotoxicity:  0.079 RPMI-8226 Immunitoxicity:  0.15
A549 Cytotoxicity:  0.446 Hek293 Cytotoxicity:  0.269
BCF:   0.508
?
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:   2.588
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.032
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.459
?
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
NPO12631 Corylus avellana Species Betulaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s10616-014-9808-y]
NPO12631 Corylus avellana Species Betulaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.stress.2021.100038]
NPO12631 Corylus avellana Species Betulaceae Eukaryota Shells; Leaves n.a. n.a. PMID[18163585]
NPO12631 Corylus avellana Species Betulaceae Eukaryota n.a. n.a. n.a. PMID[25420236]
NPO12631 Corylus avellana Species Betulaceae Eukaryota Leaves n.a. n.a. PMID[26606246]
NPO12631 Corylus avellana Species Betulaceae Eukaryota Green Leafy Covers n.a. n.a. PMID[28520428]
NPO12631 Corylus avellana Species Betulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12631 Corylus avellana Species Betulaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO12631 Corylus avellana Species Betulaceae Eukaryota n.a. n.a. Database[FooDB]
NPO12631 Corylus avellana Species Betulaceae 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
NPT1045 Cell line U2OS Homo sapiens EC50 > 150000.0 nM PMID[26606246]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. EC50 > 150000.0 nM PMID[26606246]
NPT621 Tissue Plasma Homo sapiens Inhibition = 14.4 % PMID[33616390]
NPT621 Tissue Plasma Homo sapiens Inhibition = 33.3 % PMID[33616390]

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 NPC488674 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
0.7436 Intermediate Similarity NPC473137
0.7368 Intermediate Similarity NPC488678
0.6087 Remote Similarity NPC488677
0.6042 Remote Similarity NPC488578
0.6042 Remote Similarity NPC231767
0.6042 Remote Similarity NPC608772
0.5957 Remote Similarity NPC488580
0.5957 Remote Similarity NPC127975
0.5957 Remote Similarity NPC611070
0.5833 Remote Similarity NPC488675
0.5714 Remote Similarity NPC608771
0.5417 Remote Similarity NPC31936
0.5333 Remote Similarity NPC308689
0.525 Remote Similarity NPC288411
0.5122 Remote Similarity NPC138942
0.5098 Remote Similarity NPC601260

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC488674 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