Structure

Physi-Chem Properties

Molecular Weight:  610.4
Volume:  665.106
LogP:  6.991
LogD:  4.395
LogS:  -3.463
# Rotatable Bonds:  22
TPSA:  117.12
# H-Bond Aceptor:  8
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.09
Synthetic Accessibility Score:  2.936
Fsp3:  0.556
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.875
MDCK Permeability:  2.1342279069358483e-05
Pgp-inhibitor:  0.998
Pgp-substrate:  0.303
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.996
30% Bioavailability (F30%):  0.838

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.004
Plasma Protein Binding (PPB):  100.23512268066406%
Volume Distribution (VD):  0.266
Pgp-substrate:  1.2019619941711426%

ADMET: Metabolism

CYP1A2-inhibitor:  0.075
CYP1A2-substrate:  0.698
CYP2C19-inhibitor:  0.712
CYP2C19-substrate:  0.628
CYP2C9-inhibitor:  0.606
CYP2C9-substrate:  0.957
CYP2D6-inhibitor:  0.802
CYP2D6-substrate:  0.767
CYP3A4-inhibitor:  0.842
CYP3A4-substrate:  0.175

ADMET: Excretion

Clearance (CL):  3.718
Half-life (T1/2):  0.827

ADMET: Toxicity

hERG Blockers:  0.259
Human Hepatotoxicity (H-HT):  0.414
Drug-inuced Liver Injury (DILI):  0.045
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.035
Maximum Recommended Daily Dose:  0.308
Skin Sensitization:  0.945
Carcinogencity:  0.006
Eye Corrosion:  0.003
Eye Irritation:  0.007
Respiratory Toxicity:  0.012

Download Data

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

  Natural Product: NPC27501

Natural Product ID:  NPC27501
Common Name*:   Butylcyclohexane
IUPAC Name:   butylcyclohexane
Synonyms:   Butyl-Cyclohexane
Standard InCHIKey:  GGBJHURWWWLEQH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H20/c1-2-3-7-10-8-5-4-6-9-10/h10H,2-9H2,1H3
SMILES:  CCCCC1CCCCC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL192820
PubChem CID:   15506
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004474] Saturated hydrocarbons
        • [CHEMONTID:0001016] Cycloalkanes

*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
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. fruit n.a. PMID[15739361]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. seed n.a. PMID[23845552]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota seeds n.a. n.a. PMID[23999046]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16741 Codonopsis pilosula Species Campanulaceae 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
NPT208 Individual Protein Cytochrome P450 1A2 Homo sapiens IC50 = 55000.0 nM PMID[474752]

☑ 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 NPC27501 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 NPC14312
0.8077 Intermediate Similarity NPC133792
0.8077 Intermediate Similarity NPC7777
0.8 Intermediate Similarity NPC172053
0.6818 Remote Similarity NPC82648
0.6818 Remote Similarity NPC278711
0.6818 Remote Similarity NPC227986
0.6818 Remote Similarity NPC136996
0.6818 Remote Similarity NPC64370
0.6818 Remote Similarity NPC302327
0.6818 Remote Similarity NPC273385
0.6667 Remote Similarity NPC59846
0.6667 Remote Similarity NPC252008
0.6522 Remote Similarity NPC89422
0.6364 Remote Similarity NPC224874
0.6364 Remote Similarity NPC110911
0.625 Remote Similarity NPC77249
0.625 Remote Similarity NPC154477
0.625 Remote Similarity NPC26974
0.625 Remote Similarity NPC239406
0.625 Remote Similarity NPC26229
0.5946 Remote Similarity NPC78551
0.5946 Remote Similarity NPC59570
0.5946 Remote Similarity NPC45270
0.5946 Remote Similarity NPC227632
0.5946 Remote Similarity NPC215118
0.5946 Remote Similarity NPC62086
0.5946 Remote Similarity NPC135077
0.5909 Remote Similarity NPC98925
0.5833 Remote Similarity NPC139717
0.5833 Remote Similarity NPC152459
0.5833 Remote Similarity NPC297643
0.5833 Remote Similarity NPC229262
0.5789 Remote Similarity NPC103290
0.5714 Remote Similarity NPC328441
0.5641 Remote Similarity NPC105246
0.5641 Remote Similarity NPC190232
0.5641 Remote Similarity NPC193180
0.5625 Remote Similarity NPC321646

  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 NPC27501 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
0.5641 Remote Similarity NPD390 Approved
0.5641 Remote Similarity NPD1799 Clinical (unspecified phase)
0.5641 Remote Similarity NPD718 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