Structure

Physi-Chem Properties

Molecular Weight:  96.02
Volume:  96.151
LogP:  -0.127
LogD:  0.035
LogS:  -0.464
# 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:  0.4
Synthetic Accessibility Score:  3.008
Fsp3:  0.2
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.519
MDCK Permeability:  3.4670600143726915e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.997
Plasma Protein Binding (PPB):  57.697296142578125%
Volume Distribution (VD):  0.422
Pgp-substrate:  60.26389694213867%

ADMET: Metabolism

CYP1A2-inhibitor:  0.041
CYP1A2-substrate:  0.121
CYP2C19-inhibitor:  0.037
CYP2C19-substrate:  0.309
CYP2C9-inhibitor:  0.03
CYP2C9-substrate:  0.313
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.238
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.281

ADMET: Excretion

Clearance (CL):  8.913
Half-life (T1/2):  0.892

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.317
Drug-inuced Liver Injury (DILI):  0.632
AMES Toxicity:  0.623
Rat Oral Acute Toxicity:  0.807
Maximum Recommended Daily Dose:  0.105
Skin Sensitization:  0.942
Carcinogencity:  0.834
Eye Corrosion:  0.943
Eye Irritation:  0.952
Respiratory Toxicity:  0.961

Download Data

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

  Natural Product: NPC130923

Natural Product ID:  NPC130923
Common Name*:   4-Cyclopentene-1,3-Dione
IUPAC Name:   cyclopent-4-ene-1,3-dione
Synonyms:  
Standard InCHIKey:  MCFZBCCYOPSZLG-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H4O2/c6-4-1-2-5(7)3-4/h1-2H,3H2
SMILES:  O=C1C=CC(=O)C1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL224231
PubChem CID:   70258
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000133] 1,3-dicarbonyl compounds
            • [CHEMONTID:0003926] Beta-diketones

*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
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. PMID[11520216]
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]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
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]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
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
NPT1572 Protein Family Glycogen synthase kinase-3 Homo sapiens IC50 = 12000.0 nM PMID[528439]

☑ 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 NPC130923 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
0.9167 High Similarity NPC24833
0.8537 High Similarity NPC471753
0.7727 Intermediate Similarity NPC471752
0.7568 Intermediate Similarity NPC304788
0.7561 Intermediate Similarity NPC113082
0.6957 Remote Similarity NPC100380
0.6939 Remote Similarity NPC471751
0.6905 Remote Similarity NPC217923
0.6889 Remote Similarity NPC477686
0.6809 Remote Similarity NPC324812
0.6757 Remote Similarity NPC155900
0.675 Remote Similarity NPC269641
0.6744 Remote Similarity NPC111474
0.6739 Remote Similarity NPC166788
0.6739 Remote Similarity NPC191337
0.6667 Remote Similarity NPC155880
0.6667 Remote Similarity NPC92863
0.6667 Remote Similarity NPC216921
0.6667 Remote Similarity NPC145311
0.6604 Remote Similarity NPC192843
0.6604 Remote Similarity NPC281230
0.6585 Remote Similarity NPC38497
0.6531 Remote Similarity NPC118788
0.6531 Remote Similarity NPC474391
0.6531 Remote Similarity NPC15325
0.6471 Remote Similarity NPC296311
0.6429 Remote Similarity NPC185839
0.6429 Remote Similarity NPC279300
0.6429 Remote Similarity NPC220061
0.6389 Remote Similarity NPC94980
0.6304 Remote Similarity NPC301972
0.6304 Remote Similarity NPC292463
0.6279 Remote Similarity NPC180840
0.625 Remote Similarity NPC266979
0.625 Remote Similarity NPC8610
0.625 Remote Similarity NPC262558
0.6222 Remote Similarity NPC7754
0.6222 Remote Similarity NPC270170
0.62 Remote Similarity NPC228776
0.619 Remote Similarity NPC75204
0.617 Remote Similarity NPC145755
0.617 Remote Similarity NPC25771
0.617 Remote Similarity NPC267514
0.6154 Remote Similarity NPC45283
0.6136 Remote Similarity NPC33761
0.6122 Remote Similarity NPC471958
0.6098 Remote Similarity NPC12889
0.6078 Remote Similarity NPC477458
0.6042 Remote Similarity NPC474202
0.6042 Remote Similarity NPC474362
0.6038 Remote Similarity NPC300121
0.6038 Remote Similarity NPC322461
0.6 Remote Similarity NPC101147
0.6 Remote Similarity NPC323278
0.5962 Remote Similarity NPC137396
0.5952 Remote Similarity NPC72258
0.5882 Remote Similarity NPC176819
0.5882 Remote Similarity NPC225974
0.5882 Remote Similarity NPC163984
0.5882 Remote Similarity NPC58970
0.587 Remote Similarity NPC221250
0.587 Remote Similarity NPC33489
0.5849 Remote Similarity NPC474805
0.5849 Remote Similarity NPC37644
0.5849 Remote Similarity NPC474141
0.5818 Remote Similarity NPC325977
0.5789 Remote Similarity NPC38455
0.5763 Remote Similarity NPC322457
0.5745 Remote Similarity NPC208936
0.5745 Remote Similarity NPC287397
0.5745 Remote Similarity NPC67920
0.5745 Remote Similarity NPC298710
0.5714 Remote Similarity NPC158853
0.5682 Remote Similarity NPC8416
0.5682 Remote Similarity NPC254764
0.5652 Remote Similarity NPC12319
0.5652 Remote Similarity NPC18205
0.5652 Remote Similarity NPC8270
0.5614 Remote Similarity NPC281195
0.5614 Remote Similarity NPC311852

  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 NPC130923 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
0.6136 Remote Similarity NPD5783 Phase 3
0.6087 Remote Similarity NPD9091 Suspended
0.6087 Remote Similarity NPD9297 Discontinued
0.5714 Remote Similarity NPD9090 Phase 3

  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