Structure

Physi-Chem Properties

Molecular Weight:  102.1
Volume:  121.123
LogP:  1.776
LogD:  1.619
LogS:  -1.059
# Rotatable Bonds:  3
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.571
Synthetic Accessibility Score:  2.55
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:  -4.136
MDCK Permeability:  2.749769191723317e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.03
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.008
30% Bioavailability (F30%):  0.013

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.992
Plasma Protein Binding (PPB):  57.843170166015625%
Volume Distribution (VD):  0.999
Pgp-substrate:  50.389556884765625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.527
CYP1A2-substrate:  0.825
CYP2C19-inhibitor:  0.048
CYP2C19-substrate:  0.761
CYP2C9-inhibitor:  0.02
CYP2C9-substrate:  0.375
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.348
CYP3A4-inhibitor:  0.009
CYP3A4-substrate:  0.187

ADMET: Excretion

Clearance (CL):  9.575
Half-life (T1/2):  0.758

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.029
Drug-inuced Liver Injury (DILI):  0.09
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.108
Maximum Recommended Daily Dose:  0.015
Skin Sensitization:  0.392
Carcinogencity:  0.135
Eye Corrosion:  0.903
Eye Irritation:  0.989
Respiratory Toxicity:  0.037

Download Data

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

  Natural Product: NPC276332

Natural Product ID:  NPC276332
Common Name*:   2-Methylpentan-1-Ol
IUPAC Name:   2-methylpentan-1-ol
Synonyms:  
Standard InCHIKey:  PFNHSEQQEPMLNI-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H14O/c1-3-4-6(2)5-7/h6-7H,3-5H2,1-2H3
SMILES:  CCCC(CO)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1569610
PubChem CID:   7745
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0000286] Primary 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
NPO9090 Patrinia villosa Species Caprifoliaceae Eukaryota n.a. leaf n.a. PMID[27019553]
NPO9090 Patrinia villosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20930 Patrinia scabiosifolia Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9090 Patrinia villosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9090 Patrinia villosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9090 Patrinia villosa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20930 Patrinia scabiosifolia Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9090 Patrinia villosa Species Caprifoliaceae 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
NPT210 Individual Protein Thyroid stimulating hormone receptor Homo sapiens Potency = 12589.3 nM PMID[458808]
NPT135 Individual Protein Chromobox protein homolog 1 Homo sapiens Potency n.a. 89125.1 nM PMID[458809]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 66824.2 nM PMID[458808]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 1471.6 nM PMID[458809]
NPT2 Others Unspecified Potency n.a. 68589.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 38.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 21891.1 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 30637.9 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 NPC276332 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
1.0 High Similarity NPC39869
0.88 High Similarity NPC256186
0.88 High Similarity NPC23071
0.84 Intermediate Similarity NPC52403
0.8214 Intermediate Similarity NPC52362
0.8065 Intermediate Similarity NPC283682
0.8 Intermediate Similarity NPC88839
0.7778 Intermediate Similarity NPC275462
0.7778 Intermediate Similarity NPC190797
0.76 Intermediate Similarity NPC294703
0.7576 Intermediate Similarity NPC61665
0.75 Intermediate Similarity NPC560
0.7407 Intermediate Similarity NPC87529
0.7407 Intermediate Similarity NPC245688
0.7407 Intermediate Similarity NPC199270
0.7353 Intermediate Similarity NPC177022
0.7308 Intermediate Similarity NPC110344
0.7143 Intermediate Similarity NPC213764
0.7143 Intermediate Similarity NPC232554
0.7037 Intermediate Similarity NPC39977
0.7 Intermediate Similarity NPC159845
0.7 Intermediate Similarity NPC279895
0.6944 Remote Similarity NPC221022
0.6897 Remote Similarity NPC252154
0.68 Remote Similarity NPC311000
0.6786 Remote Similarity NPC94144
0.6774 Remote Similarity NPC110884
0.6667 Remote Similarity NPC299484
0.6667 Remote Similarity NPC219266
0.6562 Remote Similarity NPC24506
0.6562 Remote Similarity NPC163556
0.6562 Remote Similarity NPC112242
0.6562 Remote Similarity NPC147096
0.6562 Remote Similarity NPC225783
0.6562 Remote Similarity NPC185041
0.6562 Remote Similarity NPC236797
0.6552 Remote Similarity NPC88887
0.6452 Remote Similarity NPC325345
0.6364 Remote Similarity NPC126915
0.6364 Remote Similarity NPC122962
0.6316 Remote Similarity NPC469759
0.6316 Remote Similarity NPC160261
0.6296 Remote Similarity NPC106054
0.6286 Remote Similarity NPC316685
0.625 Remote Similarity NPC319680
0.625 Remote Similarity NPC144891
0.6176 Remote Similarity NPC139131
0.6176 Remote Similarity NPC291158
0.6176 Remote Similarity NPC205141
0.6176 Remote Similarity NPC181516
0.6176 Remote Similarity NPC272998
0.6176 Remote Similarity NPC72324
0.6176 Remote Similarity NPC1748
0.6176 Remote Similarity NPC193062
0.6176 Remote Similarity NPC66124
0.6176 Remote Similarity NPC185538
0.6176 Remote Similarity NPC319034
0.6111 Remote Similarity NPC328441
0.6098 Remote Similarity NPC215358
0.6061 Remote Similarity NPC28077
0.6 Remote Similarity NPC140389
0.5952 Remote Similarity NPC87439
0.5952 Remote Similarity NPC24824
0.5952 Remote Similarity NPC165651
0.5952 Remote Similarity NPC473914
0.5952 Remote Similarity NPC210560
0.5946 Remote Similarity NPC252843
0.5938 Remote Similarity NPC287782
0.5926 Remote Similarity NPC163707
0.5926 Remote Similarity NPC236761
0.5882 Remote Similarity NPC197207
0.5882 Remote Similarity NPC182541
0.5882 Remote Similarity NPC280532
0.5882 Remote Similarity NPC187058
0.5882 Remote Similarity NPC267243
0.5882 Remote Similarity NPC149070
0.5882 Remote Similarity NPC127074
0.5854 Remote Similarity NPC269862
0.5833 Remote Similarity NPC97967
0.5814 Remote Similarity NPC198540
0.5814 Remote Similarity NPC287550
0.5814 Remote Similarity NPC84030
0.5814 Remote Similarity NPC223468
0.5814 Remote Similarity NPC176309
0.5814 Remote Similarity NPC147343
0.5806 Remote Similarity NPC128335
0.5806 Remote Similarity NPC190117
0.5789 Remote Similarity NPC325454
0.5789 Remote Similarity NPC473568
0.5789 Remote Similarity NPC469714
0.5789 Remote Similarity NPC38930
0.5789 Remote Similarity NPC469712
0.5758 Remote Similarity NPC151140
0.5758 Remote Similarity NPC104195
0.5758 Remote Similarity NPC122768
0.5758 Remote Similarity NPC61066
0.5714 Remote Similarity NPC12231
0.5714 Remote Similarity NPC94196
0.5714 Remote Similarity NPC152759
0.5676 Remote Similarity NPC474914
0.5676 Remote Similarity NPC474392
0.5667 Remote Similarity NPC91093
0.5667 Remote Similarity NPC114270
0.5641 Remote Similarity NPC222792
0.5641 Remote Similarity NPC3531
0.5641 Remote Similarity NPC316217
0.5625 Remote Similarity NPC320326
0.5625 Remote Similarity NPC324353
0.56 Remote Similarity NPC2724
0.56 Remote Similarity NPC110911

  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 NPC276332 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
0.68 Remote Similarity NPD8223 Approved
0.6452 Remote Similarity NPD8988 Clinical (unspecified phase)
0.6176 Remote Similarity NPD5383 Approved
0.6176 Remote Similarity NPD2272 Approved
0.5926 Remote Similarity NPD8224 Approved
0.5882 Remote Similarity NPD8814 Phase 3
0.5814 Remote Similarity NPD384 Approved
0.5814 Remote Similarity NPD385 Approved
0.5806 Remote Similarity NPD57 Approved
0.5667 Remote Similarity NPD8225 Phase 3
0.5641 Remote Similarity NPD9450 Approved
0.5641 Remote Similarity NPD9453 Phase 3
0.5641 Remote Similarity NPD77 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