Structure

Physi-Chem Properties

Molecular Weight:  88.09
Volume:  103.827
LogP:  1.023
LogD:  0.793
LogS:  -0.184
# Rotatable Bonds:  1
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.507
Synthetic Accessibility Score:  2.4
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:  -4.212
MDCK Permeability:  2.6820789571502246e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.156
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.352
30% Bioavailability (F30%):  0.311

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.932
Plasma Protein Binding (PPB):  27.196382522583008%
Volume Distribution (VD):  1.186
Pgp-substrate:  68.77120971679688%

ADMET: Metabolism

CYP1A2-inhibitor:  0.197
CYP1A2-substrate:  0.515
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.887
CYP2C9-inhibitor:  0.02
CYP2C9-substrate:  0.622
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.407
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.304

ADMET: Excretion

Clearance (CL):  10.15
Half-life (T1/2):  0.754

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.033
Drug-inuced Liver Injury (DILI):  0.11
AMES Toxicity:  0.02
Rat Oral Acute Toxicity:  0.043
Maximum Recommended Daily Dose:  0.029
Skin Sensitization:  0.088
Carcinogencity:  0.041
Eye Corrosion:  0.825
Eye Irritation:  0.99
Respiratory Toxicity:  0.033

Download Data

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

  Natural Product: NPC190797

Natural Product ID:  NPC190797
Common Name*:   3-Methylbutan-2-Ol
IUPAC Name:   3-methylbutan-2-ol
Synonyms:  
Standard InCHIKey:  MXLMTQWGSQIYOW-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H12O/c1-4(2)5(3)6/h4-6H,1-3H3
SMILES:  CC(C(C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL443470
PubChem CID:   11732
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001661] Secondary alcohols

*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
NPO23768 Camellia saluenensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23768 Camellia saluenensis Species Theaceae 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
NPT27 Others Unspecified log Ks = 1.92 n.a. PMID[459584]
NPT561 Organism Tetrahymena pyriformis Tetrahymena pyriformis GI50 = 100948530.19 nM PMID[459585]

☑ 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 NPC190797 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
0.8846 High Similarity NPC52362
0.875 High Similarity NPC23071
0.875 High Similarity NPC256186
0.8696 High Similarity NPC88839
0.8696 High Similarity NPC299484
0.8333 Intermediate Similarity NPC39977
0.8 Intermediate Similarity NPC87529
0.8 Intermediate Similarity NPC245688
0.7917 Intermediate Similarity NPC110344
0.7826 Intermediate Similarity NPC163707
0.7778 Intermediate Similarity NPC39869
0.7778 Intermediate Similarity NPC276332
0.7692 Intermediate Similarity NPC232554
0.7692 Intermediate Similarity NPC88887
0.7692 Intermediate Similarity NPC140389
0.75 Intermediate Similarity NPC294703
0.75 Intermediate Similarity NPC106054
0.7407 Intermediate Similarity NPC560
0.7391 Intermediate Similarity NPC311000
0.7308 Intermediate Similarity NPC114270
0.7308 Intermediate Similarity NPC94144
0.6923 Remote Similarity NPC52403
0.6897 Remote Similarity NPC159845
0.6786 Remote Similarity NPC252154
0.6667 Remote Similarity NPC110884
0.6667 Remote Similarity NPC152773
0.6667 Remote Similarity NPC157340
0.6667 Remote Similarity NPC270334
0.6552 Remote Similarity NPC272307
0.6552 Remote Similarity NPC320326
0.6538 Remote Similarity NPC219266
0.6429 Remote Similarity NPC275462
0.64 Remote Similarity NPC236761
0.6389 Remote Similarity NPC316217
0.6389 Remote Similarity NPC222792
0.6364 Remote Similarity NPC283682
0.6333 Remote Similarity NPC301586
0.6333 Remote Similarity NPC325345
0.6333 Remote Similarity NPC33415
0.625 Remote Similarity NPC122962
0.6176 Remote Similarity NPC316685
0.6087 Remote Similarity NPC2724
0.6071 Remote Similarity NPC199270
0.6061 Remote Similarity NPC66124
0.6061 Remote Similarity NPC72324
0.6061 Remote Similarity NPC319034
0.6061 Remote Similarity NPC193062
0.6061 Remote Similarity NPC1748
0.6 Remote Similarity NPC61665
0.6 Remote Similarity NPC328688
0.5938 Remote Similarity NPC28077
0.5926 Remote Similarity NPC83723
0.5882 Remote Similarity NPC81989
0.5862 Remote Similarity NPC304927
0.5862 Remote Similarity NPC304786
0.5862 Remote Similarity NPC272690
0.5862 Remote Similarity NPC213764
0.5862 Remote Similarity NPC289974
0.5833 Remote Similarity NPC177022
0.5806 Remote Similarity NPC261397
0.5806 Remote Similarity NPC279895
0.5758 Remote Similarity NPC267243
0.5758 Remote Similarity NPC197207
0.5758 Remote Similarity NPC182541
0.5758 Remote Similarity NPC127074
0.5758 Remote Similarity NPC149070
0.5758 Remote Similarity NPC187058
0.5758 Remote Similarity NPC317060
0.575 Remote Similarity NPC144891
0.575 Remote Similarity NPC319680
0.5714 Remote Similarity NPC97967
0.5714 Remote Similarity NPC133819
0.5714 Remote Similarity NPC191084
0.5714 Remote Similarity NPC168052
0.5714 Remote Similarity NPC250870
0.5667 Remote Similarity NPC190117
0.5667 Remote Similarity NPC230726
0.5667 Remote Similarity NPC128335
0.5625 Remote Similarity NPC122768
0.5625 Remote Similarity NPC151140
0.5625 Remote Similarity NPC104195
0.5625 Remote Similarity NPC61066
0.561 Remote Similarity NPC215358

  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 NPC190797 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
0.7826 Intermediate Similarity NPD8224 Approved
0.7391 Intermediate Similarity NPD8223 Approved
0.7308 Intermediate Similarity NPD8225 Phase 3
0.6667 Remote Similarity NPD8226 Approved
0.6429 Remote Similarity NPD8956 Approved
0.6333 Remote Similarity NPD8988 Clinical (unspecified phase)
0.6333 Remote Similarity NPD8549 Clinical (unspecified phase)
0.5926 Remote Similarity NPD8196 Approved
0.5758 Remote Similarity NPD8814 Phase 3
0.5667 Remote Similarity NPD57 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