Structure

Physi-Chem Properties

Molecular Weight:  114.1
Volume:  135.782
LogP:  1.904
LogD:  0.291
LogS:  -0.738
# 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:  0.535
Synthetic Accessibility Score:  2.245
Fsp3:  0.857
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:  -4.263
MDCK Permeability:  2.7116118872072548e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.015
20% Bioavailability (F20%):  0.786
30% Bioavailability (F30%):  0.413

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.992
Plasma Protein Binding (PPB):  69.4163589477539%
Volume Distribution (VD):  1.72
Pgp-substrate:  39.2335090637207%

ADMET: Metabolism

CYP1A2-inhibitor:  0.371
CYP1A2-substrate:  0.839
CYP2C19-inhibitor:  0.051
CYP2C19-substrate:  0.942
CYP2C9-inhibitor:  0.037
CYP2C9-substrate:  0.229
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.469
CYP3A4-inhibitor:  0.017
CYP3A4-substrate:  0.365

ADMET: Excretion

Clearance (CL):  6.642
Half-life (T1/2):  0.734

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.15
Drug-inuced Liver Injury (DILI):  0.803
AMES Toxicity:  0.208
Rat Oral Acute Toxicity:  0.069
Maximum Recommended Daily Dose:  0.021
Skin Sensitization:  0.159
Carcinogencity:  0.074
Eye Corrosion:  0.872
Eye Irritation:  0.968
Respiratory Toxicity:  0.346

Download Data

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

  Natural Product: NPC91093

Natural Product ID:  NPC91093
Common Name*:   2,4-Dimethylpentan-3-One
IUPAC Name:   2,4-dimethylpentan-3-one
Synonyms:  
Standard InCHIKey:  HXVNBWAKAOHACI-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H14O/c1-5(2)7(8)6(3)4/h5-6H,1-4H3
SMILES:  CC(C(=O)C(C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3560924
PubChem CID:   11271
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

☑ 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
NPT2 Others Unspecified Potency n.a. 21872.4 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 NPC91093 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
0.9565 High Similarity NPC307594
0.9091 High Similarity NPC83723
0.88 High Similarity NPC100997
0.875 High Similarity NPC227197
0.8182 Intermediate Similarity NPC147212
0.7857 Intermediate Similarity NPC321646
0.7826 Intermediate Similarity NPC141986
0.7727 Intermediate Similarity NPC211453
0.75 Intermediate Similarity NPC222945
0.75 Intermediate Similarity NPC32603
0.72 Intermediate Similarity NPC185768
0.72 Intermediate Similarity NPC33928
0.7143 Intermediate Similarity NPC287782
0.7097 Intermediate Similarity NPC248190
0.7 Intermediate Similarity NPC228727
0.6957 Remote Similarity NPC171188
0.6923 Remote Similarity NPC30338
0.6875 Remote Similarity NPC121215
0.6774 Remote Similarity NPC94196
0.6667 Remote Similarity NPC66624
0.6667 Remote Similarity NPC289974
0.6667 Remote Similarity NPC304927
0.6538 Remote Similarity NPC133819
0.6538 Remote Similarity NPC254524
0.6429 Remote Similarity NPC79591
0.6364 Remote Similarity NPC200333
0.6364 Remote Similarity NPC110911
0.6286 Remote Similarity NPC38930
0.6286 Remote Similarity NPC223315
0.6071 Remote Similarity NPC129976
0.6061 Remote Similarity NPC307027
0.6 Remote Similarity NPC295442
0.6 Remote Similarity NPC52362
0.5946 Remote Similarity NPC45270
0.5946 Remote Similarity NPC215118
0.5946 Remote Similarity NPC59570
0.5946 Remote Similarity NPC135077
0.5938 Remote Similarity NPC280532
0.5882 Remote Similarity NPC218357
0.5862 Remote Similarity NPC230726
0.5862 Remote Similarity NPC211250
0.5806 Remote Similarity NPC222997
0.5806 Remote Similarity NPC42403
0.5806 Remote Similarity NPC79887
0.5806 Remote Similarity NPC104195
0.5806 Remote Similarity NPC61066
0.5806 Remote Similarity NPC122768
0.5806 Remote Similarity NPC29561
0.5806 Remote Similarity NPC4962
0.5806 Remote Similarity NPC196434
0.5806 Remote Similarity NPC153439
0.5806 Remote Similarity NPC221192
0.5806 Remote Similarity NPC151140
0.5769 Remote Similarity NPC106054
0.5714 Remote Similarity NPC164646
0.5676 Remote Similarity NPC141634
0.5667 Remote Similarity NPC39869
0.5667 Remote Similarity NPC276332
0.5641 Remote Similarity NPC18397
0.5625 Remote Similarity NPC21374
0.5625 Remote Similarity NPC168982
0.56 Remote Similarity NPC152773
0.56 Remote Similarity NPC328688

  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 NPC91093 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
0.5882 Remote Similarity NPD9447 Approved
0.5667 Remote Similarity NPD8990 Clinical (unspecified phase)

  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