Structure

Physi-Chem Properties

Molecular Weight:  155.13
Volume:  172.814
LogP:  0.482
LogD:  -0.661
LogS:  0.862
# Rotatable Bonds:  0
TPSA:  29.1
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.574
Synthetic Accessibility Score:  3.08
Fsp3:  0.889
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:  -4.608
MDCK Permeability:  2.349706664972473e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.131
30% Bioavailability (F30%):  0.07

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.945
Plasma Protein Binding (PPB):  23.414825439453125%
Volume Distribution (VD):  1.141
Pgp-substrate:  81.49919891357422%

ADMET: Metabolism

CYP1A2-inhibitor:  0.011
CYP1A2-substrate:  0.183
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.924
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.449
CYP2D6-inhibitor:  0.49
CYP2D6-substrate:  0.901
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.476

ADMET: Excretion

Clearance (CL):  6.101
Half-life (T1/2):  0.808

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.175
Drug-inuced Liver Injury (DILI):  0.028
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.019
Maximum Recommended Daily Dose:  0.92
Skin Sensitization:  0.648
Carcinogencity:  0.129
Eye Corrosion:  0.316
Eye Irritation:  0.175
Respiratory Toxicity:  0.858

Download Data

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

  Natural Product: NPC133178

Natural Product ID:  NPC133178
Common Name*:   2,2,6,6-Tetramethylpiperidin-4-One
IUPAC Name:   2,2,6,6-tetramethylpiperidin-4-one
Synonyms:  
Standard InCHIKey:  JWUXJYZVKZKLTJ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H17NO/c1-8(2)5-7(11)6-9(3,4)10-8/h10H,5-6H2,1-4H3
SMILES:  CC1(C)CC(=O)CC(C)(C)N1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL117614
PubChem CID:   13220
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000195] Piperidines
        • [CHEMONTID:0001581] Piperidinones

*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
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota leaves n.a. n.a. PMID[11170659]
NPO27012 Laurencia pannosa Species Rhodomelaceae Eukaryota n.a. Malaysian n.a. PMID[11374951]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota leaves n.a. n.a. PMID[12502329]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[12628396]
NPO27072 Monochaetum vulcanicum Species Melastomataceae Eukaryota n.a. n.a. n.a. PMID[15165161]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota Hairy roots n.a. n.a. PMID[19271765]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[26285573]
NPO17223 Agelas oroides Species Agelasidae Eukaryota n.a. n.a. n.a. PMID[32072810]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[6619887]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[6631435]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7264679]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7264682]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7320741]
NPO16987 Vinca erecta Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27725 Artemisia vestita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27725 Artemisia vestita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27773 Rhododendron ovatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18030 Herba acalyphae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16987 Vinca erecta Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27725 Artemisia vestita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27648 Cereus aethiops Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17223 Agelas oroides Species Agelasidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27688 Aeonium goochiae Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27072 Monochaetum vulcanicum Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20208 Rhinogobius brunneus Species Gobiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16500 Byssochlamys spectabilis Species Thermoascaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27773 Rhododendron ovatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27262 Dryopteris inaequalis Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27191 Schistochila appendiculata Species Schistochilaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27725 Artemisia vestita Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7497 Guatteria blepharophylla Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26895 Baccharis bigelovii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22488 Leptosphaeria oraemaris Species Leptosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11140 Coprinopsis cinerea Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27569 Archangelica officinalis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27012 Laurencia pannosa Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27707 Soja hispida Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27740 Alcantara ekmaniana n.a. n.a. n.a. 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
NPT2 Others Unspecified Potency n.a. 3861.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 12.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 433.3 nM PubChem BioAssay data set
NPT27 Others Unspecified H2O2 prot = 0.5 n.a. PMID[573936]
NPT27 Others Unspecified Radiation prot = 1.1 n.a. PMID[573936]
NPT35 Others n.a. pKa n.a. 7.9 n.a. PMID[573937]

☑ 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 NPC133178 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
0.614 Remote Similarity NPC248956
0.5882 Remote Similarity NPC167301
0.587 Remote Similarity NPC321646
0.566 Remote Similarity NPC15231

  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 NPC133178 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
0.619 Remote Similarity NPD1146 Phase 2
0.6034 Remote Similarity NPD9668 Phase 2
0.5686 Remote Similarity NPD635 Phase 3
0.5686 Remote Similarity NPD636 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