Structure

Physi-Chem Properties

Molecular Weight:  138.14
Volume:  164.403
LogP:  4.8
LogD:  4.028
LogS:  -5.136
# Rotatable Bonds:  0
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.481
Synthetic Accessibility Score:  1.679
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.522
MDCK Permeability:  1.7312904674327e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.037
30% Bioavailability (F30%):  0.421

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.611
Plasma Protein Binding (PPB):  96.8902816772461%
Volume Distribution (VD):  2.618
Pgp-substrate:  1.460886836051941%

ADMET: Metabolism

CYP1A2-inhibitor:  0.574
CYP1A2-substrate:  0.644
CYP2C19-inhibitor:  0.505
CYP2C19-substrate:  0.343
CYP2C9-inhibitor:  0.395
CYP2C9-substrate:  0.717
CYP2D6-inhibitor:  0.365
CYP2D6-substrate:  0.152
CYP3A4-inhibitor:  0.218
CYP3A4-substrate:  0.18

ADMET: Excretion

Clearance (CL):  5.877
Half-life (T1/2):  0.101

ADMET: Toxicity

hERG Blockers:  0.074
Human Hepatotoxicity (H-HT):  0.09
Drug-inuced Liver Injury (DILI):  0.775
AMES Toxicity:  0.022
Rat Oral Acute Toxicity:  0.067
Maximum Recommended Daily Dose:  0.028
Skin Sensitization:  0.909
Carcinogencity:  0.071
Eye Corrosion:  0.991
Eye Irritation:  0.991
Respiratory Toxicity:  0.291

Download Data

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

  Natural Product: NPC133792

Natural Product ID:  NPC133792
Common Name*:   1,2,3,4,4A,5,6,7,8,8A-Decahydronaphthalene
IUPAC Name:   1,2,3,4,4a,5,6,7,8,8a-decahydronaphthalene
Synonyms:  
Standard InCHIKey:  NNBZCPXTIHJBJL-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H18/c1-2-6-10-8-4-3-7-9(10)5-1/h9-10H,1-8H2
SMILES:  C1CCC2CCCCC2C1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1491920
PubChem CID:   7044
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004149] Polycyclic hydrocarbons

*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
NPO10021 Nerium oleander Species Apocynaceae Eukaryota leaves Niigata City, Niigata Province, Japan 2000-Nov PMID[15730243]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota leaves n.a. n.a. PMID[16933868]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[17253842]
NPO20902 Atractylodes macrocephala Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[17432574]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota stems and twigs n.a. n.a. PMID[17595134]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota stems and twigs Niigata City, Niigata Province, Japan 2001-NOV PMID[17595134]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. rhizome n.a. PMID[18787781]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[21302967]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[27228227]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[29693393]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota Leaves; Stems n.a. n.a. PMID[9214727]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[9544564]
NPO20902 Atractylodes macrocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20902 Atractylodes macrocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20902 Atractylodes macrocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20902 Atractylodes macrocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20902 Atractylodes macrocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10021 Nerium oleander Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16087 Atractylodes lancea Species Asteraceae 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
NPT531 Individual Protein Nuclear receptor ROR-gamma Mus musculus Potency = 10000.0 nM PMID[501786]
NPT64 Individual Protein ATPase family AAA domain-containing protein 5 Homo sapiens Potency n.a. 16353.5 nM PMID[501787]
NPT135 Individual Protein Chromobox protein homolog 1 Homo sapiens Potency n.a. 79432.8 nM PMID[501787]
NPT10 Individual Protein Geminin Homo sapiens Potency n.a. 103.2 nM PMID[501787]
NPT103 Individual Protein Nuclear receptor ROR-gamma Homo sapiens Potency n.a. 66824.2 nM PMID[501786]
NPT2 Others Unspecified Potency n.a. 63929.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 56977.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 1.3 nM PubChem BioAssay data set
NPT94 Individual Protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 22387.2 nM PMID[501786]
NPT2 Others Unspecified Potency = 130.0 nM PMID[501787]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 18526.0 nM PMID[501787]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 13115.4 nM PMID[501787]

☑ 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 NPC133792 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
0.9231 High Similarity NPC7777
0.8077 Intermediate Similarity NPC27501
0.8077 Intermediate Similarity NPC14312
0.6579 Remote Similarity NPC103290
0.6552 Remote Similarity NPC172053
0.641 Remote Similarity NPC193180
0.5897 Remote Similarity NPC227632
0.5897 Remote Similarity NPC62086
0.5897 Remote Similarity NPC78551
0.5854 Remote Similarity NPC192529
0.5814 Remote Similarity NPC14552
0.561 Remote Similarity NPC105246
0.561 Remote Similarity NPC190232
0.56 Remote Similarity NPC224874

  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 NPC133792 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
0.575 Remote Similarity NPD347 Approved
0.575 Remote Similarity NPD346 Approved
0.561 Remote Similarity NPD1799 Clinical (unspecified phase)

  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