Natural Product: NPC142492

Natural Product IDNPC142492
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Cyclopentane
IUPAC Name cyclopentane
Synonyms Cyclopentane
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1370850
PubChem CID 9253
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004474] Saturated hydrocarbons
        • [CHEMONTID:0001016] Cycloalkanes

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 RGSFGYAAUTVSQA-UHFFFAOYSA-N
Standard InCHI InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2
SMILES C1CCCC1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   70.08 Volume:   86.48
?
Van der Waals volume.
Dense:   0.81 LogP:   3.03
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.465
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.167
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   5.0
TPSA:   0.0
?
Topological Polar Surface Area.
 H-Bond Acceptor:   0.0
H-Bond Donor:   0.0 Rings:   1.0
Heavy Atoms:   0.0

MedChem Properties

QED Drug-Likeness Score:   0.408 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   1.0 Fsp3:   1.0
MCE-18:   6.0
?
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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.02 Fluc inhibitor:   0.669
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.007
?
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:   1.0 Promiscuous compounds:   0.67

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.673 MDCK Permeability:   -4.727
Pgp-inhibitor:   0.666 Pgp-substrate:   0.031
PAMPA:   0.027
?
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):   0.079
20% Bioavailability (F20%):   0.157 30% Bioavailability (F30%):   0.371
50% Bioavailability (F50%):   0.241

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.816 MRP1:   0.69
Plasma Protein Binding (PPB):   79.167% Volume Distribution (VD):   0.12
Fu: 11.766%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.683
OATP1B3 inhibitor:   0.806 BCRP inhibitor:   0.403
BSEP inhibitor:   0.781

ADMET: Metabolism

CYP1A2-inhibitor:   0.19 CYP1A2-substrate:   0.007
CYP2C19-inhibitor:   0.014 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.864
CYP2D6-inhibitor:   0.003 CYP2D6-substrate:   0.055
CYP3A4-inhibitor:   0.022 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.011 CYP2C8-inhibitor:   0.528
HLM stability:   0.963
?
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):  7.875 Half-life (T1/2):  0.531

ADMET: Toxicity

hERG Blockers:  0.184 hERG Blockers (10um):  0.622
Human Hepatotoxicity (H-HT):  0.356 Drug-induced Liver Injury (DILI):  0.096
AMES Toxicity:  0.216 Rat Oral Acute Toxicity:  0.211
Maximum Recommended Daily Dose:  0.457 Skin Sensitization:  0.555
Carcinogencity:  0.313 Eye Corrosion:  0.969
Eye Irritation:  0.994 Respiratory Toxicity:  0.703
Drug-induced Neurotoxicity:  0.328 Ototoxicity:  0.188
Hematotoxicity:  0.274 Drug-induced Nephrotoxicity:  0.081
Genotoxicity:  0.001 RPMI-8226 Immunitoxicity:  0.053
A549 Cytotoxicity:  0.246 Hek293 Cytotoxicity:  0.229
BCF:   1.938
?
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:   2.865
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.753
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.254
?
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
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[12350137]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota rhizome n.a. n.a. PMID[12617587]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Rhizomes n.a. n.a. PMID[23153397]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. leaf n.a. PMID[23901173]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[28068085]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[9584408]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Rhizome Essent. Oil n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24124 Curcuma longa Species Zingiberaceae 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
NPT153 Individual protein Androgen Receptor Homo sapiens Potency n.a. 21227.6 nM PubChem BioAssay data set
NPT153 Individual protein Androgen Receptor Homo sapiens Potency n.a. 24022.7 nM PubChem BioAssay data set
NPT153 Individual protein Androgen Receptor Homo sapiens Potency n.a. 6712.7 nM PubChem BioAssay data set
NPT150 Individual protein Anthrax lethal factor Bacillus anthracis Potency = 25118.9 nM PubChem BioAssay data set

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT2 Others Unspecified n.a. Potency n.a. 29984.7 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 60342.3 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 30242.8 nM PubChem BioAssay data set
NPT2 Others Unspecified n.a. Potency n.a. 11.9 nM PubChem BioAssay data set

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
- Rattus norvegicus LD50 = 11400.0 mg/kg ToxVal
- Rattus norvegicus NOEL = 1500.0 mg/kg-day ToxVal
- Rattus norvegicus LC50 = 106.0 mg/L ToxVal
- Mus musculus LD50 = 12800.0 mg/kg ToxVal
- Mus musculus LC50 = 72.0 mg/L ToxVal
- Homo sapiens DNEL systemic = 3000.0 mg/m3 ToxVal
- Homo sapiens LEL = 43027.8 mg/m3 ToxVal
- Homo sapiens PAC-3 = 65976.0 mg/m3 ToxVal
- Homo sapiens PAC-2 = 10900.4 mg/m3 ToxVal
- Homo sapiens PAC-1 = 5163.34 mg/m3 ToxVal
- Homo sapiens MEG = 589.0 mg/m3 ToxVal
- Homo sapiens MEG = 1720.0 mg/m3 ToxVal
- Homo sapiens MEG = 5000.0 mg/m3 ToxVal
- Homo sapiens MEG = 10000.0 mg/m3 ToxVal
- Homo sapiens MEG = 40000.0 mg/m3 ToxVal

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 NPC142492 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 NPC224874
1.0 High Similarity NPC236495
0.5714 Remote Similarity NPC273385
0.5714 Remote Similarity NPC278711
0.5714 Remote Similarity NPC98925
0.5714 Remote Similarity NPC64370
0.5714 Remote Similarity NPC82648
0.5714 Remote Similarity NPC227986
0.5714 Remote Similarity NPC239406
0.5714 Remote Similarity NPC77249
0.5714 Remote Similarity NPC26974
0.5714 Remote Similarity NPC136996
0.5714 Remote Similarity NPC302327
0.5714 Remote Similarity NPC154477
0.5714 Remote Similarity NPC89422
0.5714 Remote Similarity NPC26229

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC142492 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