Natural Product: NPC183620

Natural Product IDNPC183620
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YGESMQWDYGHJFP-NSHDSACASA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003670] Aryl ketones
              • [CHEMONTID:0004296] Phenylketones
                • [CHEMONTID:0004298] Alkyl-phenylketones

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 YGESMQWDYGHJFP-NSHDSACASA-N
Standard InCHI InChI=1S/C14H19NO3/c1-18-14-8-10(5-6-12(14)16)13(17)9-11-4-2-3-7-15-11/h5-6,8,11,15-16H,2-4,7,9H2,1H3/t11-/m0/s1
SMILES COc1cc(ccc1O)C(=O)C[C@@H]1CCCCN1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   249.14 Volume:   260.409
?
Van der Waals volume.
Dense:   0.957 LogP:   1.134
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.146
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.94
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   13.0
TPSA:   58.56
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   2.0 Rings:   2.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.802 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.654 Fsp3:   0.5
MCE-18:   38.238
?
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:   0.112 Fluc inhibitor:   0.203
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.107
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.386
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.004 Promiscuous compounds:   0.312

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.312 MDCK Permeability:   -4.897
Pgp-inhibitor:   0.002 Pgp-substrate:   0.836
PAMPA:   0.186
?
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%):   0.003 30% Bioavailability (F30%):   0.037
50% Bioavailability (F50%):   0.187

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.093 MRP1:   0.804
Plasma Protein Binding (PPB):   16.567% Volume Distribution (VD):   0.232
Fu: 79.276%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.081
OATP1B3 inhibitor:   0.085 BCRP inhibitor:   0.112
BSEP inhibitor:   0.004

ADMET: Metabolism

CYP1A2-inhibitor:   0.025 CYP1A2-substrate:   0.017
CYP2C19-inhibitor:   0.212 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.588
CYP2D6-inhibitor:   0.034 CYP2D6-substrate:   0.392
CYP3A4-inhibitor:   0.003 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.041
HLM stability:   0.118
?
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):  8.934 Half-life (T1/2):  1.329

ADMET: Toxicity

hERG Blockers:  0.239 hERG Blockers (10um):  0.606
Human Hepatotoxicity (H-HT):  0.533 Drug-induced Liver Injury (DILI):  0.192
AMES Toxicity:  0.434 Rat Oral Acute Toxicity:  0.689
Maximum Recommended Daily Dose:  0.715 Skin Sensitization:  0.883
Carcinogencity:  0.164 Eye Corrosion:  0.635
Eye Irritation:  0.894 Respiratory Toxicity:  0.981
Drug-induced Neurotoxicity:  0.811 Ototoxicity:  0.199
Hematotoxicity:  0.13 Drug-induced Nephrotoxicity:  0.567
Genotoxicity:  0.099 RPMI-8226 Immunitoxicity:  0.053
A549 Cytotoxicity:  0.271 Hek293 Cytotoxicity:  0.272
BCF:   0.54
?
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:   3.175
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.18
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.571
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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
NPO13539 Thuja occidentalis Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[11000026]
NPO9055 Aspergillus novofumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[27626956]
NPO14513 Lupinus laxus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17443 Phleum pratense Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13539 Thuja occidentalis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9055 Aspergillus novofumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13539 Thuja occidentalis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13539 Thuja occidentalis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17443 Phleum pratense Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13539 Thuja occidentalis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12997 Callicarpa purpurea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9055 Aspergillus novofumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3217 Cryptocarya massoy Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11350 Lissodendoryx topsenti Species Coelosphaeridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14513 Lupinus laxus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17443 Phleum pratense Species Poaceae 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 NPC183620 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
0.5957 Remote Similarity NPC16651
0.56 Remote Similarity NPC50763
0.5319 Remote Similarity NPC32163
0.5319 Remote Similarity NPC604189
0.5179 Remote Similarity NPC908

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC183620 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
0.5098 Remote Similarity NPD824 Phase 4

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