Structure

Physi-Chem Properties

Molecular Weight:  226.16
Volume:  251.866
LogP:  0.72
LogD:  -0.156
LogS:  -0.918
# Rotatable Bonds:  8
TPSA:  51.21
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.639
Synthetic Accessibility Score:  2.567
Fsp3:  0.769
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.723
MDCK Permeability:  1.655733103689272e-05
Pgp-inhibitor:  0.896
Pgp-substrate:  0.028
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.188
30% Bioavailability (F30%):  0.939

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.655
Plasma Protein Binding (PPB):  72.60071563720703%
Volume Distribution (VD):  0.46
Pgp-substrate:  43.28303527832031%

ADMET: Metabolism

CYP1A2-inhibitor:  0.042
CYP1A2-substrate:  0.894
CYP2C19-inhibitor:  0.129
CYP2C19-substrate:  0.925
CYP2C9-inhibitor:  0.043
CYP2C9-substrate:  0.955
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.903
CYP3A4-inhibitor:  0.017
CYP3A4-substrate:  0.185

ADMET: Excretion

Clearance (CL):  5.647
Half-life (T1/2):  0.872

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.249
Drug-inuced Liver Injury (DILI):  0.105
AMES Toxicity:  0.049
Rat Oral Acute Toxicity:  0.019
Maximum Recommended Daily Dose:  0.057
Skin Sensitization:  0.105
Carcinogencity:  0.033
Eye Corrosion:  0.88
Eye Irritation:  0.847
Respiratory Toxicity:  0.034

Download Data

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

  Natural Product: NPC141634

Natural Product ID:  NPC141634
Common Name*:   6,6-Dimethylundecane-2,5,10-Trione
IUPAC Name:   6,6-dimethylundecane-2,5,10-trione
Synonyms:  
Standard InCHIKey:  ZASZETBXFSDFOD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C13H22O3/c1-10(14)6-5-9-13(3,4)12(16)8-7-11(2)15/h5-9H2,1-4H3
SMILES:  CC(=O)CCCC(C)(C)C(=O)CCC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1223695
PubChem CID:   39675
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] 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
NPO4211 Negombata corticata Species Latrunculiidae Eukaryota n.a. formosan n.a. PMID[20718475]
NPO4211 Negombata corticata Species Latrunculiidae 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
NPT82 Cell Line MDA-MB-231 Homo sapiens IC50 > 50000.0 nM PMID[551089]
NPT83 Cell Line MCF7 Homo sapiens IC50 > 50000.0 nM PMID[551089]
NPT65 Cell Line HepG2 Homo sapiens IC50 > 50000.0 nM PMID[551089]
NPT81 Cell Line A549 Homo sapiens IC50 > 50000.0 nM PMID[551089]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 50000.0 nM PMID[551089]

☑ 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 NPC141634 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
0.8205 Intermediate Similarity NPC223315
0.7857 Intermediate Similarity NPC18397
0.7805 Intermediate Similarity NPC45270
0.7805 Intermediate Similarity NPC135077
0.7805 Intermediate Similarity NPC215118
0.7805 Intermediate Similarity NPC59570
0.7778 Intermediate Similarity NPC168982
0.7674 Intermediate Similarity NPC171783
0.7556 Intermediate Similarity NPC285814
0.7556 Intermediate Similarity NPC131981
0.7556 Intermediate Similarity NPC173996
0.7556 Intermediate Similarity NPC98246
0.7556 Intermediate Similarity NPC40249
0.7556 Intermediate Similarity NPC83187
0.75 Intermediate Similarity NPC29561
0.75 Intermediate Similarity NPC153439
0.75 Intermediate Similarity NPC4962
0.75 Intermediate Similarity NPC196434
0.75 Intermediate Similarity NPC42403
0.75 Intermediate Similarity NPC221192
0.75 Intermediate Similarity NPC222997
0.75 Intermediate Similarity NPC79887
0.7391 Intermediate Similarity NPC20017
0.7391 Intermediate Similarity NPC294440
0.7297 Intermediate Similarity NPC321646
0.7234 Intermediate Similarity NPC247786
0.7234 Intermediate Similarity NPC293343
0.7234 Intermediate Similarity NPC258672
0.7222 Intermediate Similarity NPC295442
0.7222 Intermediate Similarity NPC198118
0.7222 Intermediate Similarity NPC38859
0.7105 Intermediate Similarity NPC268596
0.7105 Intermediate Similarity NPC76608
0.7105 Intermediate Similarity NPC16578
0.7105 Intermediate Similarity NPC225318
0.7105 Intermediate Similarity NPC149101
0.7083 Intermediate Similarity NPC116906
0.7073 Intermediate Similarity NPC69245
0.7 Intermediate Similarity NPC121215
0.6939 Remote Similarity NPC274182
0.6939 Remote Similarity NPC236623
0.6863 Remote Similarity NPC288296
0.6863 Remote Similarity NPC53245
0.6829 Remote Similarity NPC301919
0.675 Remote Similarity NPC248190
0.6667 Remote Similarity NPC13105
0.6667 Remote Similarity NPC79591
0.6604 Remote Similarity NPC151464
0.6604 Remote Similarity NPC143597
0.6596 Remote Similarity NPC314679
0.6585 Remote Similarity NPC218357
0.6579 Remote Similarity NPC158107
0.6538 Remote Similarity NPC202850
0.6538 Remote Similarity NPC63396
0.6486 Remote Similarity NPC100997
0.6481 Remote Similarity NPC192427
0.6415 Remote Similarity NPC200258
0.6415 Remote Similarity NPC184819
0.6415 Remote Similarity NPC275472
0.6415 Remote Similarity NPC307063
0.6389 Remote Similarity NPC66624
0.6383 Remote Similarity NPC55023
0.6364 Remote Similarity NPC127798
0.6346 Remote Similarity NPC474141
0.6327 Remote Similarity NPC477878
0.6327 Remote Similarity NPC324793
0.6296 Remote Similarity NPC474105
0.625 Remote Similarity NPC262505
0.625 Remote Similarity NPC179831
0.625 Remote Similarity NPC254713
0.625 Remote Similarity NPC259261
0.625 Remote Similarity NPC261991
0.625 Remote Similarity NPC49151
0.6226 Remote Similarity NPC319589
0.6182 Remote Similarity NPC115385
0.6182 Remote Similarity NPC267626
0.6182 Remote Similarity NPC230823
0.6182 Remote Similarity NPC55004
0.6182 Remote Similarity NPC49575
0.6154 Remote Similarity NPC22182
0.6122 Remote Similarity NPC21844
0.6111 Remote Similarity NPC30338
0.6102 Remote Similarity NPC473902
0.6087 Remote Similarity NPC325452
0.6087 Remote Similarity NPC248763
0.6078 Remote Similarity NPC305182
0.6071 Remote Similarity NPC27610
0.6071 Remote Similarity NPC56905
0.6071 Remote Similarity NPC266295
0.6071 Remote Similarity NPC94991
0.6071 Remote Similarity NPC30215
0.6038 Remote Similarity NPC296311
0.6038 Remote Similarity NPC72722
0.6034 Remote Similarity NPC60565
0.6034 Remote Similarity NPC253204
0.6034 Remote Similarity NPC475795
0.6034 Remote Similarity NPC97322
0.6 Remote Similarity NPC3531
0.5965 Remote Similarity NPC96551
0.5965 Remote Similarity NPC285594
0.5962 Remote Similarity NPC314084
0.5962 Remote Similarity NPC27438
0.5952 Remote Similarity NPC49615
0.5946 Remote Similarity NPC307594
0.5946 Remote Similarity NPC227197
0.5932 Remote Similarity NPC167256
0.5932 Remote Similarity NPC32285
0.5932 Remote Similarity NPC288253
0.5926 Remote Similarity NPC250539
0.5893 Remote Similarity NPC193695
0.5862 Remote Similarity NPC478126
0.5862 Remote Similarity NPC25853
0.5862 Remote Similarity NPC127582
0.5862 Remote Similarity NPC270042
0.5833 Remote Similarity NPC128608
0.5833 Remote Similarity NPC212210
0.5833 Remote Similarity NPC76051
0.5833 Remote Similarity NPC317128
0.5833 Remote Similarity NPC33928
0.5833 Remote Similarity NPC74845
0.5814 Remote Similarity NPC156630
0.5806 Remote Similarity NPC475523
0.58 Remote Similarity NPC236355
0.58 Remote Similarity NPC4079
0.58 Remote Similarity NPC14917
0.5778 Remote Similarity NPC305660
0.5778 Remote Similarity NPC54980
0.5778 Remote Similarity NPC201622
0.5778 Remote Similarity NPC22903
0.5769 Remote Similarity NPC228776
0.5763 Remote Similarity NPC213152
0.5738 Remote Similarity NPC476330
0.5738 Remote Similarity NPC251118
0.5738 Remote Similarity NPC215987
0.5738 Remote Similarity NPC157518
0.5738 Remote Similarity NPC470329
0.5738 Remote Similarity NPC469791
0.5738 Remote Similarity NPC306805
0.5714 Remote Similarity NPC20603
0.5714 Remote Similarity NPC469781
0.5714 Remote Similarity NPC470956
0.5676 Remote Similarity NPC91093
0.5667 Remote Similarity NPC197238
0.5667 Remote Similarity NPC165695
0.5667 Remote Similarity NPC472306
0.5667 Remote Similarity NPC202118
0.566 Remote Similarity NPC64866
0.5652 Remote Similarity NPC113928
0.5652 Remote Similarity NPC201844
0.5652 Remote Similarity NPC279026
0.5652 Remote Similarity NPC154186
0.5652 Remote Similarity NPC219536
0.5652 Remote Similarity NPC261080
0.5652 Remote Similarity NPC301696
0.5652 Remote Similarity NPC14227
0.5652 Remote Similarity NPC301585
0.5652 Remote Similarity NPC31551
0.5645 Remote Similarity NPC103734
0.5645 Remote Similarity NPC473899
0.56 Remote Similarity NPC308301

  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 NPC141634 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
0.7556 Intermediate Similarity NPD344 Approved
0.7556 Intermediate Similarity NPD345 Approved
0.7556 Intermediate Similarity NPD343 Approved
0.7442 Intermediate Similarity NPD387 Clinical (unspecified phase)
0.6596 Remote Similarity NPD634 Phase 3
0.6538 Remote Similarity NPD615 Clinical (unspecified phase)
0.6279 Remote Similarity NPD9449 Clinical (unspecified phase)
0.6226 Remote Similarity NPD3729 Clinical (unspecified phase)
0.619 Remote Similarity NPD9447 Approved
0.6 Remote Similarity NPD77 Approved
0.6 Remote Similarity NPD9450 Approved
0.5849 Remote Similarity NPD3186 Phase 1
0.5778 Remote Similarity NPD3206 Approved
0.5738 Remote Similarity NPD3171 Clinical (unspecified phase)
0.566 Remote Similarity NPD9638 Phase 2
0.5652 Remote Similarity NPD9448 Phase 2
0.5652 Remote Similarity NPD633 Phase 3
0.5645 Remote Similarity NPD4224 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