Structure

Physi-Chem Properties

Molecular Weight:  86.07
Volume:  101.19
LogP:  0.766
LogD:  -0.315
LogS:  0.06
# Rotatable Bonds:  2
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.496
Synthetic Accessibility Score:  2.361
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:  -4.253
MDCK Permeability:  3.128406387986615e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.016
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.011
30% Bioavailability (F30%):  0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.991
Plasma Protein Binding (PPB):  33.58510971069336%
Volume Distribution (VD):  0.67
Pgp-substrate:  72.1207046508789%

ADMET: Metabolism

CYP1A2-inhibitor:  0.155
CYP1A2-substrate:  0.643
CYP2C19-inhibitor:  0.034
CYP2C19-substrate:  0.704
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.282
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.773
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.227

ADMET: Excretion

Clearance (CL):  8.25
Half-life (T1/2):  0.851

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.077
Drug-inuced Liver Injury (DILI):  0.3
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.046
Maximum Recommended Daily Dose:  0.035
Skin Sensitization:  0.21
Carcinogencity:  0.039
Eye Corrosion:  0.846
Eye Irritation:  0.973
Respiratory Toxicity:  0.144

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

  Natural Product: NPC147212

Natural Product ID:  NPC147212
Common Name*:   Pentan-3-One
IUPAC Name:   pentan-3-one
Synonyms:   Pentan-3-one
Standard InCHIKey:  FDPIMTJIUBPUKL-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H10O/c1-3-5(6)4-2/h3-4H2,1-2H3
SMILES:  CCC(=O)CC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL45315
PubChem CID:   7288
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] 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
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[12932131]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[20460582]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota leaves n.a. n.a. PMID[22272932]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[25172746]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[25320841]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[8910532]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8650 Perilla frutescens Species Lamiaceae 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
NPT50 Individual Protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency = 14125.4 nM PMID[515636]
NPT53 Individual Protein 4'-phosphopantetheinyl transferase ffp Bacillus subtilis Potency = 56234.1 nM PMID[515636]
NPT55 Individual Protein Putative fructose-1,6-bisphosphate aldolase Giardia intestinalis Potency = 14091.9 nM PMID[515636]
NPT198 Individual Protein Vitamin D receptor Homo sapiens Potency n.a. 89125.1 nM PMID[515636]
NPT49 Individual Protein DNA-(apurinic or apyrimidinic site) lyase Homo sapiens Potency n.a. 35481.3 nM PMID[515636]
NPT2 Others Unspecified Potency n.a. 616.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 1095.8 nM PubChem BioAssay data set
NPT27 Others Unspecified Log C = -1.861 n.a. PMID[515635]

☑ 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 NPC147212 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
0.9474 High Similarity NPC141986
0.9444 High Similarity NPC211453
0.9 High Similarity NPC222945
0.9 High Similarity NPC32603
0.8571 High Similarity NPC33928
0.8571 High Similarity NPC185768
0.8421 Intermediate Similarity NPC171188
0.8182 Intermediate Similarity NPC30338
0.8182 Intermediate Similarity NPC91093
0.8095 Intermediate Similarity NPC83723
0.7826 Intermediate Similarity NPC66624
0.7826 Intermediate Similarity NPC307594
0.7826 Intermediate Similarity NPC227197
0.7778 Intermediate Similarity NPC200333
0.7727 Intermediate Similarity NPC254524
0.75 Intermediate Similarity NPC79591
0.72 Intermediate Similarity NPC100997
0.7083 Intermediate Similarity NPC129976
0.6923 Remote Similarity NPC295442
0.6667 Remote Similarity NPC42403
0.6667 Remote Similarity NPC79887
0.6667 Remote Similarity NPC29561
0.6667 Remote Similarity NPC164646
0.6667 Remote Similarity NPC4962
0.6667 Remote Similarity NPC221192
0.6667 Remote Similarity NPC222997
0.6667 Remote Similarity NPC153439
0.6667 Remote Similarity NPC196434
0.6522 Remote Similarity NPC37479
0.6429 Remote Similarity NPC321646
0.6429 Remote Similarity NPC168982
0.6296 Remote Similarity NPC38859
0.6296 Remote Similarity NPC198118
0.625 Remote Similarity NPC133819
0.625 Remote Similarity NPC203105
0.625 Remote Similarity NPC8187
0.6207 Remote Similarity NPC16578
0.6207 Remote Similarity NPC268596
0.6207 Remote Similarity NPC228727
0.6207 Remote Similarity NPC225318
0.6207 Remote Similarity NPC149101
0.6207 Remote Similarity NPC76608
0.6154 Remote Similarity NPC59581
0.6071 Remote Similarity NPC248139
0.6071 Remote Similarity NPC155900
0.6071 Remote Similarity NPC158107
0.6071 Remote Similarity NPC270334
0.6 Remote Similarity NPC94196
0.5909 Remote Similarity NPC152773
0.5909 Remote Similarity NPC328688
0.5909 Remote Similarity NPC1502
0.5862 Remote Similarity NPC5934
0.5862 Remote Similarity NPC302611
0.5833 Remote Similarity NPC54016
0.5806 Remote Similarity NPC127142
0.5806 Remote Similarity NPC248190
0.5806 Remote Similarity NPC7814
0.5769 Remote Similarity NPC32280
0.5769 Remote Similarity NPC41485
0.5769 Remote Similarity NPC28246
0.5769 Remote Similarity NPC289974
0.5769 Remote Similarity NPC304927
0.5714 Remote Similarity NPC287782
0.5714 Remote Similarity NPC32279
0.5625 Remote Similarity NPC121215
0.56 Remote Similarity NPC39977

  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 NPC147212 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
0.6071 Remote Similarity NPD62 Approved
0.5926 Remote Similarity NPD106 Approved
0.5909 Remote Similarity NPD8200 Phase 2
0.5862 Remote Similarity NPD8856 Phase 2
0.5833 Remote Similarity NPD8190 Phase 2
0.5833 Remote Similarity NPD8615 Phase 2
0.5833 Remote Similarity NPD8616 Clinical (unspecified phase)
0.5806 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