Structure

Physi-Chem Properties

Molecular Weight:  88.09
Volume:  103.827
LogP:  1.242
LogD:  1.191
LogS:  -0.595
# Rotatable Bonds:  1
TPSA:  9.23
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.435
Synthetic Accessibility Score:  2.06
Fsp3:  1.0
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:  -4.133
MDCK Permeability:  2.3427615815307945e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.07
30% Bioavailability (F30%):  0.107

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.903
Plasma Protein Binding (PPB):  48.558956146240234%
Volume Distribution (VD):  1.256
Pgp-substrate:  68.33930969238281%

ADMET: Metabolism

CYP1A2-inhibitor:  0.208
CYP1A2-substrate:  0.497
CYP2C19-inhibitor:  0.055
CYP2C19-substrate:  0.896
CYP2C9-inhibitor:  0.013
CYP2C9-substrate:  0.357
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.691
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.216

ADMET: Excretion

Clearance (CL):  9.053
Half-life (T1/2):  0.86

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.029
Drug-inuced Liver Injury (DILI):  0.131
AMES Toxicity:  0.033
Rat Oral Acute Toxicity:  0.039
Maximum Recommended Daily Dose:  0.07
Skin Sensitization:  0.167
Carcinogencity:  0.883
Eye Corrosion:  0.299
Eye Irritation:  0.97
Respiratory Toxicity:  0.038

Download Data

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

  Natural Product: NPC328688

Natural Product ID:  NPC328688
Common Name*:   2-Methoxy-2-Methylpropane
IUPAC Name:   2-methoxy-2-methylpropane
Synonyms:  
Standard InCHIKey:  BZLVMXJERCGZMT-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H12O/c1-5(2,3)6-4/h1-4H3
SMILES:  COC(C)(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1452799
PubChem CID:   15413
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000254] Ethers
          • [CHEMONTID:0001167] Dialkyl ethers

*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
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. Nigeria(latitude 80°N and longitude 4°E) 2005; 2006 DOI[10.1002/ejlt.201000080]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11306-010-0259-y]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11306-014-0638-x]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.phytol.2008.07.007]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seeds Plovdiv, Plovdiv region in South Bulgaria DOI[10.1051/CTV/20163101031]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[11170689]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. fruit n.a. PMID[11312782]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. leaf n.a. PMID[11312782]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[11408943]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. fruit n.a. PMID[12105962]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. Esuela Tecnica Superior de Ingenieros Agrónomos de Albacete 2007 PMID[19256538]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[20826702]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[23759170]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Stalks n.a. n.a. PMID[24521157]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seeds Benedictine Pannonhalma Archabbey, Hungary PMID[29803478]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[31433178]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Leaf Essent. Oil n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Fruits n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17024 Vitis vinifera Species Vitaceae 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
NPT94 Individual Protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 17782.8 nM PMID[468970]
NPT2 Others Unspecified Potency n.a. 1689 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 59929.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 33.4 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 NPC328688 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
0.7895 Intermediate Similarity NPC152773
0.7143 Intermediate Similarity NPC106054
0.6364 Remote Similarity NPC61373
0.619 Remote Similarity NPC211453
0.6087 Remote Similarity NPC110344
0.6087 Remote Similarity NPC88839
0.6087 Remote Similarity NPC83726
0.6087 Remote Similarity NPC299484
0.6087 Remote Similarity NPC83723
0.6 Remote Similarity NPC35155
0.6 Remote Similarity NPC190797
0.5909 Remote Similarity NPC163707
0.5909 Remote Similarity NPC43196
0.5909 Remote Similarity NPC147212
0.5909 Remote Similarity NPC327092
0.5862 Remote Similarity NPC228727
0.5833 Remote Similarity NPC39977
0.5833 Remote Similarity NPC133819
0.5833 Remote Similarity NPC208021
0.5833 Remote Similarity NPC8187
0.5769 Remote Similarity NPC201132
0.5769 Remote Similarity NPC127134
0.5652 Remote Similarity NPC141986
0.5652 Remote Similarity NPC294703
0.56 Remote Similarity NPC58351
0.56 Remote Similarity NPC87529
0.56 Remote Similarity NPC256186
0.56 Remote Similarity NPC84750
0.56 Remote Similarity NPC110107
0.56 Remote Similarity NPC245688
0.56 Remote Similarity NPC91093
0.56 Remote Similarity NPC23071
0.56 Remote Similarity NPC94144
0.56 Remote Similarity NPC8368

  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 NPC328688 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
0.6842 Remote Similarity NPD8547 Phase 2
0.6538 Remote Similarity NPD8970 Approved
0.6538 Remote Similarity NPD125 Approved
0.6 Remote Similarity NPD8956 Approved
0.5909 Remote Similarity NPD8224 Approved
0.5769 Remote Similarity NPD8989 Approved
0.5714 Remote Similarity NPD9191 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