Structure

Physi-Chem Properties

Molecular Weight:  112.05
Volume:  116.083
LogP:  0.519
LogD:  0.747
LogS:  -1.454
# Rotatable Bonds:  0
TPSA:  34.14
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.429
Synthetic Accessibility Score:  3.201
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.458
MDCK Permeability:  3.2117801310960203e-05
Pgp-inhibitor:  0.011
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.034

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.989
Plasma Protein Binding (PPB):  61.349212646484375%
Volume Distribution (VD):  0.344
Pgp-substrate:  52.97583770751953%

ADMET: Metabolism

CYP1A2-inhibitor:  0.319
CYP1A2-substrate:  0.64
CYP2C19-inhibitor:  0.089
CYP2C19-substrate:  0.556
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.374
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.528
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.276

ADMET: Excretion

Clearance (CL):  8.104
Half-life (T1/2):  0.7

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.121
Drug-inuced Liver Injury (DILI):  0.304
AMES Toxicity:  0.628
Rat Oral Acute Toxicity:  0.373
Maximum Recommended Daily Dose:  0.067
Skin Sensitization:  0.46
Carcinogencity:  0.215
Eye Corrosion:  0.613
Eye Irritation:  0.974
Respiratory Toxicity:  0.494

Download Data

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

  Natural Product: NPC248190

Natural Product ID:  NPC248190
Common Name*:   3-Methylcyclopentane-1,2-Dione
IUPAC Name:   3-methylcyclopentane-1,2-dione
Synonyms:  
Standard InCHIKey:  OACYKCIZDVVNJL-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H8O2/c1-4-2-3-5(7)6(4)8/h4H,2-3H2,1H3
SMILES:  CC1CCC(=O)C1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL371371
PubChem CID:   61209
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
NPO28679 Prunus mume Species Rosaceae Eukaryota flowers n.a. n.a. PMID[12193020]
NPO28679 Prunus mume Species Rosaceae Eukaryota fruits n.a. n.a. PMID[24485782]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28679 Prunus mume Species Rosaceae 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
NPT203 Individual Protein Carboxylesterase 2 Homo sapiens Ki > 100000.0 nM PMID[546535]
NPT166 Individual Protein Acyl coenzyme A:cholesterol acyltransferase Homo sapiens Ki > 100000.0 nM PMID[546535]
NPT2610 Individual Protein Acyl coenzyme A:cholesterol acyltransferase Oryctolagus cuniculus Ki = 15700.0 nM PMID[546535]
NPT204 Individual Protein Acetylcholinesterase Homo sapiens Ki > 100000.0 nM PMID[546535]
NPT439 Individual Protein Butyrylcholinesterase Homo sapiens Ki > 100000.0 nM PMID[546535]
NPT2 Others Unspecified Potency n.a. 1149 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 36.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 18210.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 4535.4 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 NPC248190 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
0.9091 High Similarity NPC121215
0.8065 Intermediate Similarity NPC100997
0.7838 Intermediate Similarity NPC223315
0.75 Intermediate Similarity NPC18397
0.7419 Intermediate Similarity NPC307594
0.7419 Intermediate Similarity NPC227197
0.7188 Intermediate Similarity NPC79591
0.7097 Intermediate Similarity NPC91093
0.7097 Intermediate Similarity NPC30338
0.7045 Intermediate Similarity NPC20017
0.6875 Remote Similarity NPC66624
0.6857 Remote Similarity NPC321646
0.6774 Remote Similarity NPC33928
0.6774 Remote Similarity NPC254524
0.675 Remote Similarity NPC141634
0.6585 Remote Similarity NPC135077
0.6585 Remote Similarity NPC45270
0.6585 Remote Similarity NPC59570
0.6585 Remote Similarity NPC215118
0.6579 Remote Similarity NPC218357
0.6452 Remote Similarity NPC222945
0.6452 Remote Similarity NPC83723
0.6452 Remote Similarity NPC32603
0.6444 Remote Similarity NPC131981
0.6444 Remote Similarity NPC285814
0.6444 Remote Similarity NPC40249
0.6444 Remote Similarity NPC173996
0.6444 Remote Similarity NPC98246
0.6444 Remote Similarity NPC83187
0.6389 Remote Similarity NPC168982
0.6364 Remote Similarity NPC129976
0.6304 Remote Similarity NPC294440
0.6286 Remote Similarity NPC287782
0.6286 Remote Similarity NPC295442
0.625 Remote Similarity NPC185768
0.625 Remote Similarity NPC252843
0.6216 Remote Similarity NPC228727
0.62 Remote Similarity NPC319589
0.617 Remote Similarity NPC247786
0.617 Remote Similarity NPC293343
0.617 Remote Similarity NPC258672
0.6136 Remote Similarity NPC171783
0.6129 Remote Similarity NPC141986
0.6111 Remote Similarity NPC4962
0.6111 Remote Similarity NPC221192
0.6111 Remote Similarity NPC153439
0.6111 Remote Similarity NPC29561
0.6111 Remote Similarity NPC42403
0.6111 Remote Similarity NPC222997
0.6111 Remote Similarity NPC79887
0.6111 Remote Similarity NPC196434
0.6098 Remote Similarity NPC38930
0.6053 Remote Similarity NPC94196
0.6047 Remote Similarity NPC248763
0.6047 Remote Similarity NPC325452
0.5952 Remote Similarity NPC3531
0.5918 Remote Similarity NPC274182
0.5882 Remote Similarity NPC53245
0.5882 Remote Similarity NPC288296
0.587 Remote Similarity NPC282440
0.5854 Remote Similarity NPC69245
0.5833 Remote Similarity NPC38859
0.5833 Remote Similarity NPC198118
0.5806 Remote Similarity NPC59846
0.5806 Remote Similarity NPC147212
0.5789 Remote Similarity NPC16578
0.5789 Remote Similarity NPC225318
0.5789 Remote Similarity NPC149101
0.5789 Remote Similarity NPC76608
0.5789 Remote Similarity NPC280532
0.5789 Remote Similarity NPC268596
0.5745 Remote Similarity NPC4079
0.5745 Remote Similarity NPC14917
0.5745 Remote Similarity NPC236355
0.5714 Remote Similarity NPC325454
0.5714 Remote Similarity NPC59581
0.5686 Remote Similarity NPC474141
0.5676 Remote Similarity NPC158107
0.566 Remote Similarity NPC143597
0.566 Remote Similarity NPC151464
0.5625 Remote Similarity NPC91962
0.5625 Remote Similarity NPC13105
0.561 Remote Similarity NPC301919

  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 NPC248190 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
0.6667 Remote Similarity NPD9449 Clinical (unspecified phase)
0.6579 Remote Similarity NPD9447 Approved
0.6444 Remote Similarity NPD345 Approved
0.6444 Remote Similarity NPD344 Approved
0.6444 Remote Similarity NPD343 Approved
0.5952 Remote Similarity NPD77 Approved
0.5952 Remote Similarity NPD9450 Approved
0.5814 Remote Similarity NPD9635 Discontinued

  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