Structure

Physi-Chem Properties

Molecular Weight:  168.19
Volume:  207.552
LogP:  6.477
LogD:  3.813
LogS:  -6.437
# Rotatable Bonds:  0
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.492
Synthetic Accessibility Score:  1.0
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:  -4.773
MDCK Permeability:  1.6104926544358023e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.27
30% Bioavailability (F30%):  0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.515
Plasma Protein Binding (PPB):  97.4797592163086%
Volume Distribution (VD):  3.22
Pgp-substrate:  1.7393347024917603%

ADMET: Metabolism

CYP1A2-inhibitor:  0.7
CYP1A2-substrate:  0.203
CYP2C19-inhibitor:  0.494
CYP2C19-substrate:  0.067
CYP2C9-inhibitor:  0.149
CYP2C9-substrate:  0.94
CYP2D6-inhibitor:  0.112
CYP2D6-substrate:  0.111
CYP3A4-inhibitor:  0.138
CYP3A4-substrate:  0.058

ADMET: Excretion

Clearance (CL):  3.944
Half-life (T1/2):  0.122

ADMET: Toxicity

hERG Blockers:  0.162
Human Hepatotoxicity (H-HT):  0.021
Drug-inuced Liver Injury (DILI):  0.353
AMES Toxicity:  0.027
Rat Oral Acute Toxicity:  0.044
Maximum Recommended Daily Dose:  0.043
Skin Sensitization:  0.955
Carcinogencity:  0.075
Eye Corrosion:  0.992
Eye Irritation:  0.971
Respiratory Toxicity:  0.869

Download Data

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

  Natural Product: NPC224874

Natural Product ID:  NPC224874
Common Name*:   Cyclododecane
IUPAC Name:   cyclododecane
Synonyms:  
Standard InCHIKey:  DDTBPAQBQHZRDW-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H24/c1-2-4-6-8-10-12-11-9-7-5-3-1/h1-12H2
SMILES:  C1CCCCCCCCCCC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3185808
PubChem CID:   9268
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
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. PMID[11520216]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[11914965]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[27116034]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[29667821]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26429 Capsella bursa-pastoris Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26429 Capsella bursa-pastoris Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26429 Capsella bursa-pastoris Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26650 Terminalia chebula Species Combretaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21963 Hypericum japonicum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26429 Capsella bursa-pastoris Species Brassicaceae 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
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 6754.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 38 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 13477.5 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 NPC224874 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
0.9333 High Similarity NPC302327
0.9333 High Similarity NPC278711
0.9333 High Similarity NPC82648
0.9333 High Similarity NPC136996
0.9333 High Similarity NPC227986
0.9333 High Similarity NPC64370
0.9333 High Similarity NPC273385
0.875 High Similarity NPC89422
0.8235 Intermediate Similarity NPC154477
0.8235 Intermediate Similarity NPC26229
0.8235 Intermediate Similarity NPC77249
0.8235 Intermediate Similarity NPC239406
0.8235 Intermediate Similarity NPC26974
0.8 Intermediate Similarity NPC98925
0.7 Intermediate Similarity NPC127355
0.7 Intermediate Similarity NPC234888
0.6667 Remote Similarity NPC47161
0.6667 Remote Similarity NPC150271
0.6364 Remote Similarity NPC14312
0.6364 Remote Similarity NPC27501
0.625 Remote Similarity NPC236495
0.6087 Remote Similarity NPC172053
0.6087 Remote Similarity NPC38513
0.6087 Remote Similarity NPC287807
0.6 Remote Similarity NPC187095
0.5833 Remote Similarity NPC287191
0.5833 Remote Similarity NPC29199
0.5833 Remote Similarity NPC266144
0.5833 Remote Similarity NPC256060
0.5833 Remote Similarity NPC266539
0.5833 Remote Similarity NPC31891
0.5625 Remote Similarity NPC142492
0.56 Remote Similarity NPC7777
0.56 Remote Similarity NPC133792

  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 NPC224874 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