Structure

Physi-Chem Properties

Molecular Weight:  86.11
Volume:  112.332
LogP:  3.792
LogD:  3.513
LogS:  -3.673
# Rotatable Bonds:  3
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.463
Synthetic Accessibility Score:  1.209
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.183
MDCK Permeability:  2.015967038460076e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.861
30% Bioavailability (F30%):  0.972

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.991
Plasma Protein Binding (PPB):  89.96240234375%
Volume Distribution (VD):  2.128
Pgp-substrate:  13.383084297180176%

ADMET: Metabolism

CYP1A2-inhibitor:  0.962
CYP1A2-substrate:  0.853
CYP2C19-inhibitor:  0.394
CYP2C19-substrate:  0.834
CYP2C9-inhibitor:  0.263
CYP2C9-substrate:  0.828
CYP2D6-inhibitor:  0.031
CYP2D6-substrate:  0.211
CYP3A4-inhibitor:  0.03
CYP3A4-substrate:  0.155

ADMET: Excretion

Clearance (CL):  8.202
Half-life (T1/2):  0.52

ADMET: Toxicity

hERG Blockers:  0.043
Human Hepatotoxicity (H-HT):  0.018
Drug-inuced Liver Injury (DILI):  0.069
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.14
Maximum Recommended Daily Dose:  0.025
Skin Sensitization:  0.433
Carcinogencity:  0.105
Eye Corrosion:  0.992
Eye Irritation:  0.987
Respiratory Toxicity:  0.463

Download Data

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

  Natural Product: NPC150271

Natural Product ID:  NPC150271
Common Name*:   Hexane
IUPAC Name:   hexane
Synonyms:   Hexane
Standard InCHIKey:  VLKZOEOYAKHREP-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H14/c1-3-5-6-4-2/h3-6H2,1-2H3
SMILES:  CCCCCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL15939
PubChem CID:   8058
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004474] Saturated hydrocarbons
        • [CHEMONTID:0002500] Alkanes

*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
NPO7576 NPC150271 Other Stem 0.004 0.004 0.004 mg/100g Database [DUKE]

☑ 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
NPT116 Cell Line HL-60 Homo sapiens IC50 > 300.0 ug.mL-1 PMID[529898]
NPT2 Others Unspecified Potency n.a. 21623.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 3878.6 nM PubChem BioAssay data set
NPT35 Others n.a. Log S = -3.84 n.a. PMID[529891]
NPT27 Others Unspecified Log BB = 0.8 n.a. PMID[529892]
NPT35 Others n.a. LogP = 3.9 n.a. PMID[529893]
NPT27 Others Unspecified Log P16 = 4.49 n.a. PMID[529893]
NPT27 Others Unspecified Log Palk = 4.58 n.a. PMID[529893]
NPT35 Others n.a. -Log Sw = 3.84 n.a. PMID[529893]
NPT27 Others Unspecified logP(lung) = -0.21 n.a. PMID[529895]
NPT27 Others Unspecified logK(blood) = 0.21 n.a. PMID[529895]
NPT27 Others Unspecified logK(lung) = 0.0 n.a. PMID[529895]
NPT35 Others n.a. LogP = 3.868 n.a. PMID[529896]
NPT593 Organism Bursaphelenchus xylophilus Bursaphelenchus xylophilus mortality = 4.4 % PMID[529897]

☑ 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 NPC150271 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
0.9091 High Similarity NPC187095
0.8462 Intermediate Similarity NPC98925
0.7692 Intermediate Similarity NPC236495
0.7333 Intermediate Similarity NPC136996
0.7333 Intermediate Similarity NPC227986
0.7333 Intermediate Similarity NPC273385
0.7333 Intermediate Similarity NPC302327
0.7333 Intermediate Similarity NPC82648
0.7333 Intermediate Similarity NPC278711
0.7333 Intermediate Similarity NPC64370
0.6923 Remote Similarity NPC142492
0.6875 Remote Similarity NPC89422
0.6667 Remote Similarity NPC110911
0.6667 Remote Similarity NPC224874
0.6471 Remote Similarity NPC26229
0.6471 Remote Similarity NPC154477
0.6471 Remote Similarity NPC266796
0.6471 Remote Similarity NPC239406
0.6471 Remote Similarity NPC26974
0.6471 Remote Similarity NPC77249
0.6111 Remote Similarity NPC59846
0.6 Remote Similarity NPC131214
0.5882 Remote Similarity NPC170434
0.5882 Remote Similarity NPC152459

  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 NPC150271 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
NPD

  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