Structure

Physi-Chem Properties

Molecular Weight:  70.08
Volume:  86.48
LogP:  2.874
LogD:  2.178
LogS:  -2.68
# Rotatable Bonds:  0
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.408
Synthetic Accessibility Score:  1.0
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.372
MDCK Permeability:  2.394113107584417e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.47
30% Bioavailability (F30%):  0.964

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.997
Plasma Protein Binding (PPB):  79.72518157958984%
Volume Distribution (VD):  1.393
Pgp-substrate:  30.65553855895996%

ADMET: Metabolism

CYP1A2-inhibitor:  0.948
CYP1A2-substrate:  0.686
CYP2C19-inhibitor:  0.36
CYP2C19-substrate:  0.451
CYP2C9-inhibitor:  0.153
CYP2C9-substrate:  0.877
CYP2D6-inhibitor:  0.018
CYP2D6-substrate:  0.364
CYP3A4-inhibitor:  0.02
CYP3A4-substrate:  0.125

ADMET: Excretion

Clearance (CL):  6.497
Half-life (T1/2):  0.469

ADMET: Toxicity

hERG Blockers:  0.044
Human Hepatotoxicity (H-HT):  0.032
Drug-inuced Liver Injury (DILI):  0.18
AMES Toxicity:  0.049
Rat Oral Acute Toxicity:  0.278
Maximum Recommended Daily Dose:  0.038
Skin Sensitization:  0.898
Carcinogencity:  0.378
Eye Corrosion:  0.989
Eye Irritation:  0.992
Respiratory Toxicity:  0.869

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC142492

Natural Product ID:  NPC142492
Common Name*:   Cyclopentane
IUPAC Name:   cyclopentane
Synonyms:   Cyclopentane
Standard InCHIKey:  RGSFGYAAUTVSQA-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2
SMILES:  C1CCCC1
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

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  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 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 Essential Oil 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 NP ID 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

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 PMID[524651]
NPT2 Others Unspecified Potency n.a. 29984.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 60342.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 30242.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 11.9 nM PubChem BioAssay data set
NPT35 Others n.a. LogP = 2.795 n.a. PMID[524652]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  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>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.75 Intermediate Similarity NPC187095
0.6923 Remote Similarity NPC150271
0.6429 Remote Similarity NPC236495
0.6111 Remote Similarity NPC59846
0.6 Remote Similarity NPC98925
0.5625 Remote Similarity NPC224874
0.5625 Remote Similarity NPC110911

  Chemically structural similarity: II. 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>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

  Bioactivity similarity: Similar Natural Products in NPASS

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