Natural Product: NPC31090

Natural Product IDNPC31090
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ZPSGREUUQGTKDE-ZICOIJLXSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11118018
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000195] Piperidines
        • [CHEMONTID:0000335] N-acylpiperidines

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 ZPSGREUUQGTKDE-ZICOIJLXSA-N
Standard InCHI InChI=1S/C15H25NO/c1-2-3-4-5-6-7-9-12-15(17)16-13-10-8-11-14-16/h6-7,9,12H,2-5,8,10-11,13-14H2,1H3/b7-6+,12-9+
SMILES CCCCC/C=C/C=C/C(=O)N1CCCCC1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   235.19 Volume:   271.317
?
Van der Waals volume.
Dense:   0.867 LogP:   3.784
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.388
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.85
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   9.0
TPSA:   20.31
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   0.0 Rings:   1.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.39 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.298 Fsp3:   0.667
MCE-18:   7.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.066 Fluc inhibitor:   0.705
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.029
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.338
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.438 Promiscuous compounds:   0.017

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.697 MDCK Permeability:   -4.672
Pgp-inhibitor:   0.898 Pgp-substrate:   0.113
PAMPA:   0.005
?
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):   0.022
20% Bioavailability (F20%):   0.049 30% Bioavailability (F30%):   0.331
50% Bioavailability (F50%):   0.405

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.005 MRP1:   0.242
Plasma Protein Binding (PPB):   97.824% Volume Distribution (VD):   -0.481
Fu: 2.04%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.806
OATP1B3 inhibitor:   0.942 BCRP inhibitor:   0.086
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.437 CYP1A2-substrate:   0.995
CYP2C19-inhibitor:   0.559 CYP2C19-substrate:   0.982
CYP2C9-inhibitor:   0.594 CYP2C9-substrate:   0.783
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.79
CYP3A4-inhibitor:   0.004 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.074 CYP2C8-inhibitor:   1.0
HLM stability:   0.989
?
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):  6.61 Half-life (T1/2):  0.436

ADMET: Toxicity

hERG Blockers:  0.447 hERG Blockers (10um):  0.578
Human Hepatotoxicity (H-HT):  0.623 Drug-induced Liver Injury (DILI):  0.375
AMES Toxicity:  0.574 Rat Oral Acute Toxicity:  0.221
Maximum Recommended Daily Dose:  0.567 Skin Sensitization:  0.915
Carcinogencity:  0.266 Eye Corrosion:  0.291
Eye Irritation:  0.893 Respiratory Toxicity:  0.819
Drug-induced Neurotoxicity:  0.497 Ototoxicity:  0.306
Hematotoxicity:  0.317 Drug-induced Nephrotoxicity:  0.534
Genotoxicity:  0.034 RPMI-8226 Immunitoxicity:  0.094
A549 Cytotoxicity:  0.216 Hek293 Cytotoxicity:  0.481
BCF:   1.266
?
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:   4.07
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.291
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.859
?
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
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. fruit n.a. DOI[10.1016/S0040-4039(01)00209-X]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[10575373]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota roots and stolons n.a. n.a. PMID[14738379]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota dried aerial organs n.a. n.a. PMID[14738379]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota dried aerial organs n.a. n.a. PMID[14738379]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota underground organs n.a. n.a. PMID[14738379]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota leaves n.a. n.a. PMID[14738379]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. leaf n.a. PMID[15467205]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. whole plant n.a. PMID[16808005]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[23102654]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[31096694]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[31103896]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[31766491]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31815461]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[37420038]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[38067483]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[38474459]
NPO27802 Candida albicaus Species Debaryomycetaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18647 Achillea falcata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28039 Alstonia vitiensis Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28928 Piper nigrum Species Piperaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. Database[FooDB]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. Database[FooDB]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18647 Achillea falcata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27802 Candida albicaus Species Debaryomycetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28039 Alstonia vitiensis Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21334 Artemisia dracunculus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28928 Piper nigrum Species Piperaceae 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 NPC31090 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
1.0 High Similarity NPC252684
1.0 High Similarity NPC206660
0.9655 High Similarity NPC385
0.9355 High Similarity NPC42477
0.9333 High Similarity NPC133923
0.7222 Intermediate Similarity NPC34672
0.5455 Remote Similarity NPC209232

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC31090 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
0.5667 Remote Similarity NPD866 Clinical (unspecified phase)

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