Natural Product: NPC326866

Natural Product IDNPC326866
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 NOOLISFMXDJSKH-RCAUJQPQSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5319369
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001401] Menthane monoterpenoids

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 NOOLISFMXDJSKH-RCAUJQPQSA-N
Standard InCHI InChI=1S/C10H20O/c1-7(2)9-5-4-8(3)6-10(9)11/h7-11H,4-6H2,1-3H3/t8-,9?,10-/m1/s1
SMILES CC1CCC(C(C1)O)C(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   156.15 Volume:   181.75
?
Van der Waals volume.
Dense:   0.859 LogP:   3.259
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.024
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.578
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   6.0
TPSA:   20.23
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   1.0 Rings:   1.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.618 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.353 Fsp3:   1.0
MCE-18:   18.2
?
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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.038 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.004
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.82 Promiscuous compounds:   0.045

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.877 MDCK Permeability:   -4.614
Pgp-inhibitor:   0.073 Pgp-substrate:   0.06
PAMPA:   0.225
?
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):   0.012
20% Bioavailability (F20%):   0.015 30% Bioavailability (F30%):   0.068
50% Bioavailability (F50%):   0.675

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.676 MRP1:   0.897
Plasma Protein Binding (PPB):   78.846% Volume Distribution (VD):   0.376
Fu: 20.425%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.191
OATP1B3 inhibitor:   0.567 BCRP inhibitor:   0.142
BSEP inhibitor:   0.274

ADMET: Metabolism

CYP1A2-inhibitor:   0.055 CYP1A2-substrate:   0.372
CYP2C19-inhibitor:   0.841 CYP2C19-substrate:   0.167
CYP2C9-inhibitor:   0.718 CYP2C9-substrate:   0.042
CYP2D6-inhibitor:   0.01 CYP2D6-substrate:   0.032
CYP3A4-inhibitor:   0.644 CYP3A4-substrate:   0.718
CYP2B6-substrate:   0.284 CYP2C8-inhibitor:   0.796
HLM stability:   0.663
?
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):  12.58 Half-life (T1/2):  1.373

ADMET: Toxicity

hERG Blockers:  0.153 hERG Blockers (10um):  0.678
Human Hepatotoxicity (H-HT):  0.651 Drug-induced Liver Injury (DILI):  0.123
AMES Toxicity:  0.196 Rat Oral Acute Toxicity:  0.168
Maximum Recommended Daily Dose:  0.201 Skin Sensitization:  0.443
Carcinogencity:  0.383 Eye Corrosion:  0.964
Eye Irritation:  0.981 Respiratory Toxicity:  0.511
Drug-induced Neurotoxicity:  0.323 Ototoxicity:  0.566
Hematotoxicity:  0.328 Drug-induced Nephrotoxicity:  0.25
Genotoxicity:  0.001 RPMI-8226 Immunitoxicity:  0.065
A549 Cytotoxicity:  0.138 Hek293 Cytotoxicity:  0.1
BCF:   1.679
?
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:   3.358
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.574
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.014
?
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
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota leaves n.a. n.a. PMID[22272932]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[25320841]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. leaf n.a. PMID[25340465]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25340465]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25577087]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[30827604]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[37331322]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[38719900]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO31056 Mentha haplocalyx Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12405 Descurainia sophia Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12405 Descurainia sophia Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31056 Mentha haplocalyx Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12405 Descurainia sophia Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO31056 Mentha haplocalyx Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12405 Descurainia sophia Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8650.3 Perilla frutescens (l.) britt. var. crispa (thunb.) hand.-mazz. Varieties Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12405 Descurainia sophia Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2345 Coriandrum sativum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12405 Descurainia sophia Species Brassicaceae 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 NPC326866 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 NPC287550
1.0 High Similarity NPC223468
1.0 High Similarity NPC176309
1.0 High Similarity NPC147343
1.0 High Similarity NPC84030
1.0 High Similarity NPC601778
0.5652 Remote Similarity NPC67508
0.5652 Remote Similarity NPC84824

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC326866 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
1.0 High Similarity NPD384 Phase 4
1.0 High Similarity NPD385 Phase 3

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