Structure

Physi-Chem Properties

Molecular Weight:  182.17
Volume:  213.706
LogP:  3.817
LogD:  3.377
LogS:  -3.168
# 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:  0.556
Synthetic Accessibility Score:  2.111
Fsp3:  0.917
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:  -4.696
MDCK Permeability:  1.6363663235097192e-05
Pgp-inhibitor:  0.412
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.993
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.993
Plasma Protein Binding (PPB):  91.75789642333984%
Volume Distribution (VD):  0.992
Pgp-substrate:  5.065479755401611%

ADMET: Metabolism

CYP1A2-inhibitor:  0.765
CYP1A2-substrate:  0.405
CYP2C19-inhibitor:  0.411
CYP2C19-substrate:  0.066
CYP2C9-inhibitor:  0.307
CYP2C9-substrate:  0.921
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.441
CYP3A4-inhibitor:  0.08
CYP3A4-substrate:  0.077

ADMET: Excretion

Clearance (CL):  5.515
Half-life (T1/2):  0.73

ADMET: Toxicity

hERG Blockers:  0.068
Human Hepatotoxicity (H-HT):  0.109
Drug-inuced Liver Injury (DILI):  0.101
AMES Toxicity:  0.041
Rat Oral Acute Toxicity:  0.048
Maximum Recommended Daily Dose:  0.058
Skin Sensitization:  0.795
Carcinogencity:  0.174
Eye Corrosion:  0.874
Eye Irritation:  0.978
Respiratory Toxicity:  0.809

Download Data

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

  Natural Product: NPC38859

Natural Product ID:  NPC38859
Common Name*:   Cyclododecanone
IUPAC Name:   cyclododecanone
Synonyms:  
Standard InCHIKey:  SXVPOSFURRDKBO-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H22O/c13-12-10-8-6-4-2-1-3-5-7-9-11-12/h1-11H2
SMILES:  O=C1CCCCCCCCCCC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1883853
PubChem CID:   13246
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
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Flower buds n.a. n.a. PMID[12880307]
NPO25825 Saussurea lappa Species Asteraceae Eukaryota Roots n.a. n.a. PMID[14510592]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Stems n.a. n.a. PMID[17663584]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Roots n.a. n.a. PMID[18186611]
NPO30603 Saussurea lappa n.a. n.a. n.a. n.a. root n.a. PMID[18409040]
NPO30603 Saussurea lappa n.a. n.a. n.a. roots n.a. n.a. PMID[18579374]
NPO30603 Saussurea lappa n.a. n.a. n.a. n.a. n.a. n.a. PMID[25068579]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Steamed Roots n.a. n.a. PMID[26200131]
NPO25825 Saussurea lappa Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[3572418]
NPO30603 Saussurea lappa n.a. n.a. n.a. n.a. root n.a. PMID[8541643]
NPO14105.2 Panax pseudo-ginseng var. notoginseng Varieties Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14148.1 Panax pseudo - ginseng var. notoginseng Varieties Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30603 Saussurea lappa n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO25825 Saussurea lappa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14105.2 Panax pseudo-ginseng var. notoginseng Varieties Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14105.3 Panax pseudo-ginseng wall. var. notoginseng (burk.) hoo et tseng Varieties Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25825 Saussurea lappa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25825 Saussurea lappa 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
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 8.9 nM PMID[487794]
NPT106 Individual Protein Peroxisome proliferator-activated receptor delta Homo sapiens Potency n.a. 9771.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 30606.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 61068.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 54947.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 27278.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68589.6 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 NPC38859 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 NPC198118
0.963 High Similarity NPC221192
0.963 High Similarity NPC153439
0.963 High Similarity NPC196434
0.963 High Similarity NPC222997
0.963 High Similarity NPC4962
0.963 High Similarity NPC42403
0.963 High Similarity NPC29561
0.963 High Similarity NPC79887
0.9286 High Similarity NPC168982
0.9259 High Similarity NPC295442
0.8966 High Similarity NPC16578
0.8966 High Similarity NPC225318
0.8966 High Similarity NPC76608
0.8966 High Similarity NPC149101
0.8966 High Similarity NPC268596
0.8929 High Similarity NPC158107
0.8148 Intermediate Similarity NPC66624
0.7879 Intermediate Similarity NPC301919
0.7857 Intermediate Similarity NPC79591
0.7742 Intermediate Similarity NPC262505
0.7742 Intermediate Similarity NPC254713
0.7742 Intermediate Similarity NPC261991
0.7742 Intermediate Similarity NPC49151
0.7742 Intermediate Similarity NPC179831
0.75 Intermediate Similarity NPC129976
0.7429 Intermediate Similarity NPC223315
0.7273 Intermediate Similarity NPC49615
0.7222 Intermediate Similarity NPC141634
0.7143 Intermediate Similarity NPC30338
0.7037 Intermediate Similarity NPC32603
0.7027 Intermediate Similarity NPC45270
0.7027 Intermediate Similarity NPC215118
0.7027 Intermediate Similarity NPC135077
0.7027 Intermediate Similarity NPC59570
0.6875 Remote Similarity NPC321646
0.6786 Remote Similarity NPC33928
0.6786 Remote Similarity NPC254524
0.6774 Remote Similarity NPC32279
0.6667 Remote Similarity NPC69245
0.6667 Remote Similarity NPC141986
0.6667 Remote Similarity NPC18397
0.6571 Remote Similarity NPC156630
0.65 Remote Similarity NPC76051
0.65 Remote Similarity NPC74845
0.6486 Remote Similarity NPC201622
0.6486 Remote Similarity NPC305660
0.6486 Remote Similarity NPC54980
0.6486 Remote Similarity NPC22903
0.6452 Remote Similarity NPC100997
0.6429 Remote Similarity NPC222945
0.6341 Remote Similarity NPC469781
0.6316 Remote Similarity NPC261080
0.6316 Remote Similarity NPC279026
0.6316 Remote Similarity NPC301696
0.6316 Remote Similarity NPC301585
0.6316 Remote Similarity NPC294085
0.6316 Remote Similarity NPC118968
0.6316 Remote Similarity NPC14227
0.6316 Remote Similarity NPC223249
0.6316 Remote Similarity NPC183424
0.6316 Remote Similarity NPC31551
0.6316 Remote Similarity NPC154186
0.6316 Remote Similarity NPC219536
0.6316 Remote Similarity NPC201844
0.6316 Remote Similarity NPC214610
0.6316 Remote Similarity NPC113928
0.6296 Remote Similarity NPC147212
0.625 Remote Similarity NPC473674
0.6216 Remote Similarity NPC220061
0.6207 Remote Similarity NPC185768
0.6154 Remote Similarity NPC250028
0.6154 Remote Similarity NPC165533
0.6154 Remote Similarity NPC256163
0.6154 Remote Similarity NPC161097
0.6154 Remote Similarity NPC12156
0.6154 Remote Similarity NPC48930
0.6154 Remote Similarity NPC149299
0.6154 Remote Similarity NPC28598
0.6154 Remote Similarity NPC40597
0.6129 Remote Similarity NPC59581
0.6111 Remote Similarity NPC218357
0.6098 Remote Similarity NPC317128
0.6098 Remote Similarity NPC171783
0.6053 Remote Similarity NPC268826
0.6047 Remote Similarity NPC285814
0.6047 Remote Similarity NPC83187
0.6047 Remote Similarity NPC131981
0.6047 Remote Similarity NPC173996
0.6047 Remote Similarity NPC98246
0.6047 Remote Similarity NPC40249
0.6 Remote Similarity NPC171736
0.6 Remote Similarity NPC196924
0.6 Remote Similarity NPC216630
0.6 Remote Similarity NPC209970
0.6 Remote Similarity NPC141914
0.6 Remote Similarity NPC307783
0.6 Remote Similarity NPC53541
0.6 Remote Similarity NPC149184
0.5952 Remote Similarity NPC287231
0.5952 Remote Similarity NPC47363
0.5926 Remote Similarity NPC211453
0.5909 Remote Similarity NPC294440
0.5897 Remote Similarity NPC80234
0.5854 Remote Similarity NPC203531
0.5854 Remote Similarity NPC236579
0.5854 Remote Similarity NPC67462
0.5833 Remote Similarity NPC248190
0.5814 Remote Similarity NPC63182
0.5814 Remote Similarity NPC145045
0.5814 Remote Similarity NPC52700
0.5814 Remote Similarity NPC105329
0.5806 Remote Similarity NPC227197
0.5806 Remote Similarity NPC307594
0.5778 Remote Similarity NPC145311
0.5778 Remote Similarity NPC293343
0.5778 Remote Similarity NPC247786
0.5778 Remote Similarity NPC258672
0.5714 Remote Similarity NPC19305
0.5714 Remote Similarity NPC255837
0.5682 Remote Similarity NPC326957
0.5682 Remote Similarity NPC324004
0.5682 Remote Similarity NPC328497
0.5676 Remote Similarity NPC121215
0.5652 Remote Similarity NPC116906
0.5652 Remote Similarity NPC474391
0.5641 Remote Similarity NPC92863
0.5641 Remote Similarity NPC155880
0.561 Remote Similarity NPC103286
0.561 Remote Similarity NPC163746
0.561 Remote Similarity NPC474361

  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 NPC38859 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
0.6486 Remote Similarity NPD3206 Approved
0.6316 Remote Similarity NPD633 Phase 3
0.6316 Remote Similarity NPD9448 Phase 2
0.6316 Remote Similarity NPD9655 Approved
0.6047 Remote Similarity NPD345 Approved
0.6047 Remote Similarity NPD343 Approved
0.6047 Remote Similarity NPD344 Approved
0.6 Remote Similarity NPD2270 Approved
0.5952 Remote Similarity NPD2699 Approved
0.5854 Remote Similarity NPD387 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