Structure

Physi-Chem Properties

Molecular Weight:  86.11
Volume:  112.332
LogP:  3.669
LogD:  3.972
LogS:  -3.581
# Rotatable Bonds:  2
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.484
Synthetic Accessibility Score:  1.893
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:  -4.122
MDCK Permeability:  2.622030660859309e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.01
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.103
30% Bioavailability (F30%):  0.705

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.988
Plasma Protein Binding (PPB):  87.6016616821289%
Volume Distribution (VD):  1.724
Pgp-substrate:  11.813516616821289%

ADMET: Metabolism

CYP1A2-inhibitor:  0.938
CYP1A2-substrate:  0.806
CYP2C19-inhibitor:  0.283
CYP2C19-substrate:  0.893
CYP2C9-inhibitor:  0.413
CYP2C9-substrate:  0.901
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.147
CYP3A4-inhibitor:  0.021
CYP3A4-substrate:  0.209

ADMET: Excretion

Clearance (CL):  9.419
Half-life (T1/2):  0.561

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.026
Drug-inuced Liver Injury (DILI):  0.117
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.109
Maximum Recommended Daily Dose:  0.029
Skin Sensitization:  0.253
Carcinogencity:  0.145
Eye Corrosion:  0.991
Eye Irritation:  0.992
Respiratory Toxicity:  0.223

Download Data

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

  Natural Product: NPC110911

Natural Product ID:  NPC110911
Common Name*:   2-Methylpentane
IUPAC Name:   2-methylpentane
Synonyms:   2-Methyl-Pentane; 2-Methylpentane
Standard InCHIKey:  AFABGHUZZDYHJO-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H14/c1-4-5-6(2)3/h6H,4-5H2,1-3H3
SMILES:  CCCC(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL30909
PubChem CID:   7892
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004474] Saturated hydrocarbons
        • [CHEMONTID:0002500] Alkanes
          • [CHEMONTID:0004620] Branched 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

☑ 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. 196.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 69287.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 44079.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 30949.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 19689.5 nM PubChem BioAssay data set
NPT27 Others Unspecified Log BB = 0.97 n.a. PMID[505409]
NPT419 Organism Oryctolagus cuniculus Oryctolagus cuniculus MES = 0.26 n.a. PMID[505410]
NPT27 Others Unspecified logP(lung) = 0.29 n.a. PMID[505411]
NPT27 Others Unspecified logK(blood) = -0.39 n.a. PMID[505411]
NPT27 Others Unspecified logK(lung) = -0.1 n.a. PMID[505411]
NPT35 Others n.a. LogP = 3.738 n.a. PMID[505412]

☑ 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 NPC110911 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
0.7778 Intermediate Similarity NPC252008
0.7778 Intermediate Similarity NPC59846
0.7143 Intermediate Similarity NPC187095
0.6875 Remote Similarity NPC131214
0.6667 Remote Similarity NPC152459
0.6667 Remote Similarity NPC150271
0.6364 Remote Similarity NPC14312
0.6364 Remote Similarity NPC91093
0.6364 Remote Similarity NPC27501
0.6087 Remote Similarity NPC172053
0.6087 Remote Similarity NPC307594
0.5882 Remote Similarity NPC98925
0.5625 Remote Similarity NPC142492
0.56 Remote Similarity NPC276332
0.56 Remote Similarity NPC39869
0.56 Remote Similarity NPC100997

  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 NPC110911 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