Structure

Physi-Chem Properties

Molecular Weight:  126.1
Volume:  144.522
LogP:  1.93
LogD:  1.515
LogS:  -1.206
# Rotatable Bonds:  0
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.486
Synthetic Accessibility Score:  1.887
Fsp3:  0.875
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.551
MDCK Permeability:  2.107377804350108e-05
Pgp-inhibitor:  0.675
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.958
30% Bioavailability (F30%):  0.974

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.998
Plasma Protein Binding (PPB):  57.86174011230469%
Volume Distribution (VD):  0.758
Pgp-substrate:  44.371150970458984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.632
CYP1A2-substrate:  0.79
CYP2C19-inhibitor:  0.181
CYP2C19-substrate:  0.178
CYP2C9-inhibitor:  0.12
CYP2C9-substrate:  0.864
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.709
CYP3A4-inhibitor:  0.022
CYP3A4-substrate:  0.121

ADMET: Excretion

Clearance (CL):  6.968
Half-life (T1/2):  0.865

ADMET: Toxicity

hERG Blockers:  0.027
Human Hepatotoxicity (H-HT):  0.143
Drug-inuced Liver Injury (DILI):  0.128
AMES Toxicity:  0.158
Rat Oral Acute Toxicity:  0.068
Maximum Recommended Daily Dose:  0.065
Skin Sensitization:  0.382
Carcinogencity:  0.198
Eye Corrosion:  0.881
Eye Irritation:  0.984
Respiratory Toxicity:  0.383

Download Data

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

  Natural Product: NPC158107

Natural Product ID:  NPC158107
Common Name*:   Cyclooctanone
IUPAC Name:   cyclooctanone
Synonyms:   Cyclooctanone
Standard InCHIKey:  IIRFCWANHMSDCG-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H14O/c9-8-6-4-2-1-3-5-7-8/h1-7H2
SMILES:  O=C1CCCCCCC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL18737
PubChem CID:   10403
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003487] Cyclic ketones

*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
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[12350137]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota rhizome n.a. n.a. PMID[12617587]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. leaf n.a. PMID[15388977]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. stem n.a. PMID[17202689]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. pericarp n.a. PMID[20628994]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Rhizomes n.a. n.a. PMID[23153397]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. leaf n.a. PMID[23901173]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[24175626]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[28068085]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[9584408]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Rhizome Essent. Oil n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8698 Zanthoxylum schinifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8698 Zanthoxylum schinifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8698 Zanthoxylum schinifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8698 Zanthoxylum schinifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9290 Zanthoxylum piperitum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24124 Curcuma longa Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5315 Zanthoxylum bungeanum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8698 Zanthoxylum schinifolium Species Rutaceae 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
NPT1528 Individual Protein Phenylethanolamine N-methyltransferase Bos taurus IC50 = 72000.0 nM PMID[506210]
NPT24039 SINGLE PROTEIN E3 ubiquitin-protein ligase TRIM33 Homo sapiens IC50 = 249.8 nM PMID[506211]
NPT24040 SINGLE PROTEIN Transcription intermediary factor 1-alpha Homo sapiens IC50 = 166.3 nM PMID[506211]

☑ 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 NPC158107 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
0.8929 High Similarity NPC38859
0.8929 High Similarity NPC198118
0.8621 High Similarity NPC29561
0.8621 High Similarity NPC153439
0.8621 High Similarity NPC196434
0.8621 High Similarity NPC222997
0.8621 High Similarity NPC79887
0.8621 High Similarity NPC221192
0.8621 High Similarity NPC4962
0.8621 High Similarity NPC42403
0.8333 Intermediate Similarity NPC168982
0.8276 Intermediate Similarity NPC295442
0.8065 Intermediate Similarity NPC268596
0.8065 Intermediate Similarity NPC225318
0.8065 Intermediate Similarity NPC76608
0.8065 Intermediate Similarity NPC16578
0.8065 Intermediate Similarity NPC149101
0.7857 Intermediate Similarity NPC66624
0.7586 Intermediate Similarity NPC79591
0.7241 Intermediate Similarity NPC129976
0.7143 Intermediate Similarity NPC301919
0.697 Remote Similarity NPC49151
0.697 Remote Similarity NPC262505
0.697 Remote Similarity NPC254713
0.697 Remote Similarity NPC261991
0.697 Remote Similarity NPC179831
0.6897 Remote Similarity NPC30338
0.6786 Remote Similarity NPC32603
0.6757 Remote Similarity NPC223315
0.6579 Remote Similarity NPC141634
0.6571 Remote Similarity NPC49615
0.6562 Remote Similarity NPC32279
0.6552 Remote Similarity NPC33928
0.6552 Remote Similarity NPC254524
0.6429 Remote Similarity NPC141986
0.641 Remote Similarity NPC135077
0.641 Remote Similarity NPC215118
0.641 Remote Similarity NPC45270
0.641 Remote Similarity NPC59570
0.6389 Remote Similarity NPC156630
0.625 Remote Similarity NPC100997
0.6207 Remote Similarity NPC222945
0.6176 Remote Similarity NPC321646
0.6098 Remote Similarity NPC473674
0.6098 Remote Similarity NPC18397
0.6071 Remote Similarity NPC147212
0.6053 Remote Similarity NPC220061
0.6053 Remote Similarity NPC69245
0.6 Remote Similarity NPC185768
0.5952 Remote Similarity NPC171783
0.5952 Remote Similarity NPC74845
0.5952 Remote Similarity NPC76051
0.5938 Remote Similarity NPC59581
0.5897 Remote Similarity NPC54980
0.5897 Remote Similarity NPC201622
0.5897 Remote Similarity NPC22903
0.5897 Remote Similarity NPC268826
0.5897 Remote Similarity NPC305660
0.5814 Remote Similarity NPC469781
0.575 Remote Similarity NPC14227
0.575 Remote Similarity NPC279026
0.575 Remote Similarity NPC113928
0.575 Remote Similarity NPC183424
0.575 Remote Similarity NPC294085
0.575 Remote Similarity NPC154186
0.575 Remote Similarity NPC201844
0.575 Remote Similarity NPC301696
0.575 Remote Similarity NPC223249
0.575 Remote Similarity NPC118968
0.575 Remote Similarity NPC219536
0.575 Remote Similarity NPC31551
0.575 Remote Similarity NPC214610
0.575 Remote Similarity NPC301585
0.575 Remote Similarity NPC261080
0.5714 Remote Similarity NPC211453
0.5676 Remote Similarity NPC248190
0.5625 Remote Similarity NPC307594
0.5625 Remote Similarity NPC227197
0.561 Remote Similarity NPC28598
0.561 Remote Similarity NPC250028
0.561 Remote Similarity NPC165533
0.561 Remote Similarity NPC40597
0.561 Remote Similarity NPC48930
0.561 Remote Similarity NPC161097
0.561 Remote Similarity NPC149299
0.561 Remote Similarity NPC12156
0.561 Remote Similarity NPC256163

  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 NPC158107 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
0.5897 Remote Similarity NPD3206 Approved
0.575 Remote Similarity NPD9655 Approved
0.575 Remote Similarity NPD633 Phase 3
0.575 Remote Similarity NPD9448 Phase 2

  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