Structure

Physi-Chem Properties

Molecular Weight:  84.06
Volume:  92.634
LogP:  0.403
LogD:  -0.163
LogS:  0.178
# Rotatable Bonds:  0
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.43
Synthetic Accessibility Score:  2.113
Fsp3:  0.8
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:  -4.378
MDCK Permeability:  2.7423189749242738e-05
Pgp-inhibitor:  0.028
Pgp-substrate:  0.012
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.013
30% Bioavailability (F30%):  0.021

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.993
Plasma Protein Binding (PPB):  31.865276336669922%
Volume Distribution (VD):  0.723
Pgp-substrate:  74.29352569580078%

ADMET: Metabolism

CYP1A2-inhibitor:  0.187
CYP1A2-substrate:  0.789
CYP2C19-inhibitor:  0.048
CYP2C19-substrate:  0.368
CYP2C9-inhibitor:  0.018
CYP2C9-substrate:  0.683
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.824
CYP3A4-inhibitor:  0.009
CYP3A4-substrate:  0.176

ADMET: Excretion

Clearance (CL):  7.549
Half-life (T1/2):  0.889

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.18
Drug-inuced Liver Injury (DILI):  0.116
AMES Toxicity:  0.444
Rat Oral Acute Toxicity:  0.071
Maximum Recommended Daily Dose:  0.067
Skin Sensitization:  0.188
Carcinogencity:  0.133
Eye Corrosion:  0.882
Eye Irritation:  0.987
Respiratory Toxicity:  0.206

Download Data

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

  Natural Product: NPC254524

Natural Product ID:  NPC254524
Common Name*:   Cyclopentanone
IUPAC Name:   cyclopentanone
Synonyms:   Cyclopentanone
Standard InCHIKey:  BGTOWKSIORTVQH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H8O/c6-5-3-1-2-4-5/h1-4H2
SMILES:  C1CCC(=O)C1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL18620
PubChem CID:   8452
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003487] Cyclic ketones

*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
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/hlca.19270100148]
NPO9445 Crocus sativus Species Iridaceae Eukaryota Petals n.a. n.a. PMID[15043425]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. PMID[24338885]
NPO9445 Crocus sativus Species Iridaceae Eukaryota Silk Stigma Style n.a. n.a. Database[FooDB]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9445 Crocus sativus Species Iridaceae 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
NPT1528 Individual Protein Phenylethanolamine N-methyltransferase Bos taurus IC50 > 1000000.0 nM PMID[521169]
NPT27 Others Unspecified LC50 = 43752210.52 nM PMID[521171]
NPT610 Others Molecular identity unknown Ratio = 101.07 n.a. PMID[521172]
NPT610 Others Molecular identity unknown Ratio = 113.72 n.a. PMID[521172]
NPT610 Others Molecular identity unknown Ratio = 129.19 n.a. PMID[521172]
NPT610 Others Molecular identity unknown Ratio = 82.79 n.a. PMID[521172]
NPT24039 SINGLE PROTEIN E3 ubiquitin-protein ligase TRIM33 Homo sapiens IC50 = 233.5 nM PMID[521173]
NPT24040 SINGLE PROTEIN Transcription intermediary factor 1-alpha Homo sapiens IC50 = 135.8 nM PMID[521173]
NPT2 Others Unspecified Potency n.a. 1112.1 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 69567.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 442.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68589.6 nM PubChem BioAssay data set

☑ 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 NPC254524 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
0.8182 Intermediate Similarity NPC141986
0.7917 Intermediate Similarity NPC30338
0.7826 Intermediate Similarity NPC32603
0.7826 Intermediate Similarity NPC222945
0.7727 Intermediate Similarity NPC147212
0.76 Intermediate Similarity NPC66624
0.76 Intermediate Similarity NPC129976
0.75 Intermediate Similarity NPC33928
0.75 Intermediate Similarity NPC185768
0.7308 Intermediate Similarity NPC79591
0.7273 Intermediate Similarity NPC211453
0.7037 Intermediate Similarity NPC100997
0.6923 Remote Similarity NPC227197
0.6923 Remote Similarity NPC307594
0.6786 Remote Similarity NPC198118
0.6786 Remote Similarity NPC38859
0.6786 Remote Similarity NPC295442
0.6774 Remote Similarity NPC248190
0.6562 Remote Similarity NPC121215
0.6552 Remote Similarity NPC42403
0.6552 Remote Similarity NPC79887
0.6552 Remote Similarity NPC221192
0.6552 Remote Similarity NPC4962
0.6552 Remote Similarity NPC158107
0.6552 Remote Similarity NPC29561
0.6552 Remote Similarity NPC196434
0.6552 Remote Similarity NPC153439
0.6552 Remote Similarity NPC222997
0.6538 Remote Similarity NPC91093
0.6538 Remote Similarity NPC164646
0.6522 Remote Similarity NPC171188
0.64 Remote Similarity NPC83723
0.6333 Remote Similarity NPC168982
0.6129 Remote Similarity NPC76608
0.6129 Remote Similarity NPC225318
0.6129 Remote Similarity NPC268596
0.6129 Remote Similarity NPC16578
0.6129 Remote Similarity NPC149101
0.6071 Remote Similarity NPC59581
0.6 Remote Similarity NPC223315
0.6 Remote Similarity NPC248139
0.5909 Remote Similarity NPC200333
0.5806 Remote Similarity NPC321646
0.5769 Remote Similarity NPC37479
0.5758 Remote Similarity NPC7814
0.5758 Remote Similarity NPC127142
0.5667 Remote Similarity NPC32279
0.5667 Remote Similarity NPC287782
0.5625 Remote Similarity NPC228727

  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 NPC254524 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
0.6 Remote Similarity NPD62 Approved
0.5758 Remote Similarity NPD8857 Approved

  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