Structure

Physi-Chem Properties

Molecular Weight:  126.1
Volume:  150.442
LogP:  2.369
LogD:  2.165
LogS:  -2.032
# Rotatable Bonds:  5
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.408
Synthetic Accessibility Score:  2.21
Fsp3:  0.625
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.376
MDCK Permeability:  2.34579620155273e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.008
30% Bioavailability (F30%):  0.022

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.997
Plasma Protein Binding (PPB):  74.28287506103516%
Volume Distribution (VD):  0.873
Pgp-substrate:  35.8361701965332%

ADMET: Metabolism

CYP1A2-inhibitor:  0.593
CYP1A2-substrate:  0.723
CYP2C19-inhibitor:  0.175
CYP2C19-substrate:  0.835
CYP2C9-inhibitor:  0.097
CYP2C9-substrate:  0.845
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.346
CYP3A4-inhibitor:  0.026
CYP3A4-substrate:  0.275

ADMET: Excretion

Clearance (CL):  8.017
Half-life (T1/2):  0.814

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.37
Drug-inuced Liver Injury (DILI):  0.392
AMES Toxicity:  0.561
Rat Oral Acute Toxicity:  0.921
Maximum Recommended Daily Dose:  0.048
Skin Sensitization:  0.919
Carcinogencity:  0.824
Eye Corrosion:  0.984
Eye Irritation:  0.988
Respiratory Toxicity:  0.972

Download Data

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

  Natural Product: NPC220061

Natural Product ID:  NPC220061
Common Name*:   Oct-1-En-3-One
IUPAC Name:   oct-1-en-3-one
Synonyms:  
Standard InCHIKey:  KLTVSWGXIAYTHO-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H14O/c1-3-5-6-7-8(9)4-2/h4H,2-3,5-7H2,1H3
SMILES:  CCCCCC(=O)C=C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3186486
PubChem CID:   61346
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0003131] Alpha,beta-unsaturated carbonyl compounds
            • [CHEMONTID:0003672] Alpha,beta-unsaturated ketones
              • [CHEMONTID:0001363] Enones

*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

☑ 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
NPT2 Others Unspecified Potency n.a. 7.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 2031.2 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 NPC220061 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
0.7941 Intermediate Similarity NPC155900
0.7727 Intermediate Similarity NPC324812
0.7692 Intermediate Similarity NPC92863
0.7692 Intermediate Similarity NPC155880
0.75 Intermediate Similarity NPC217923
0.7442 Intermediate Similarity NPC25771
0.7391 Intermediate Similarity NPC474391
0.7317 Intermediate Similarity NPC113082
0.7209 Intermediate Similarity NPC292463
0.7174 Intermediate Similarity NPC145311
0.7111 Intermediate Similarity NPC100380
0.7059 Intermediate Similarity NPC94980
0.6977 Remote Similarity NPC473674
0.6905 Remote Similarity NPC48930
0.6875 Remote Similarity NPC477458
0.6818 Remote Similarity NPC301972
0.6765 Remote Similarity NPC66624
0.675 Remote Similarity NPC38497
0.6744 Remote Similarity NPC270170
0.6744 Remote Similarity NPC7754
0.6739 Remote Similarity NPC471752
0.6735 Remote Similarity NPC471751
0.6667 Remote Similarity NPC267514
0.6667 Remote Similarity NPC176819
0.6667 Remote Similarity NPC145755
0.6667 Remote Similarity NPC15325
0.6667 Remote Similarity NPC471753
0.6667 Remote Similarity NPC32351
0.6667 Remote Similarity NPC295442
0.6667 Remote Similarity NPC163984
0.6667 Remote Similarity NPC58970
0.6596 Remote Similarity NPC91962
0.6585 Remote Similarity NPC24833
0.6585 Remote Similarity NPC185839
0.6571 Remote Similarity NPC79591
0.6538 Remote Similarity NPC325977
0.6531 Remote Similarity NPC64866
0.6522 Remote Similarity NPC191337
0.6522 Remote Similarity NPC239754
0.6486 Remote Similarity NPC196434
0.6486 Remote Similarity NPC153439
0.6486 Remote Similarity NPC4962
0.6486 Remote Similarity NPC79887
0.6486 Remote Similarity NPC221192
0.6486 Remote Similarity NPC29561
0.6486 Remote Similarity NPC42403
0.6486 Remote Similarity NPC222997
0.6444 Remote Similarity NPC216921
0.6429 Remote Similarity NPC180840
0.6429 Remote Similarity NPC130923
0.6383 Remote Similarity NPC236355
0.6383 Remote Similarity NPC4079
0.6383 Remote Similarity NPC110234
0.6383 Remote Similarity NPC8610
0.6383 Remote Similarity NPC262558
0.6383 Remote Similarity NPC14917
0.6383 Remote Similarity NPC44363
0.6383 Remote Similarity NPC163751
0.6364 Remote Similarity NPC33489
0.6327 Remote Similarity NPC228776
0.6316 Remote Similarity NPC168982
0.6304 Remote Similarity NPC477686
0.6296 Remote Similarity NPC311852
0.6279 Remote Similarity NPC33761
0.6275 Remote Similarity NPC37644
0.6275 Remote Similarity NPC296311
0.6275 Remote Similarity NPC45283
0.6275 Remote Similarity NPC268564
0.625 Remote Similarity NPC216130
0.6222 Remote Similarity NPC287397
0.6222 Remote Similarity NPC67920
0.6222 Remote Similarity NPC298710
0.6216 Remote Similarity NPC38859
0.6216 Remote Similarity NPC198118
0.62 Remote Similarity NPC27438
0.62 Remote Similarity NPC234829
0.6182 Remote Similarity NPC274927
0.6182 Remote Similarity NPC106851
0.617 Remote Similarity NPC474362
0.617 Remote Similarity NPC166788
0.617 Remote Similarity NPC474202
0.6154 Remote Similarity NPC16578
0.6154 Remote Similarity NPC225318
0.6154 Remote Similarity NPC322461
0.6154 Remote Similarity NPC149101
0.6154 Remote Similarity NPC76608
0.6154 Remote Similarity NPC268596
0.6136 Remote Similarity NPC111474
0.6111 Remote Similarity NPC115385
0.6098 Remote Similarity NPC269641
0.6071 Remote Similarity NPC235242
0.6071 Remote Similarity NPC251042
0.6071 Remote Similarity NPC122521
0.6071 Remote Similarity NPC229252
0.6071 Remote Similarity NPC143857
0.6071 Remote Similarity NPC174447
0.6053 Remote Similarity NPC158107
0.6038 Remote Similarity NPC200258
0.6038 Remote Similarity NPC275472
0.6 Remote Similarity NPC320421
0.6 Remote Similarity NPC473487
0.6 Remote Similarity NPC30338
0.6 Remote Similarity NPC224227
0.6 Remote Similarity NPC118788
0.6 Remote Similarity NPC30215
0.5965 Remote Similarity NPC40082
0.5962 Remote Similarity NPC474141
0.5926 Remote Similarity NPC473733
0.5926 Remote Similarity NPC477201
0.5918 Remote Similarity NPC471958
0.5918 Remote Similarity NPC180534
0.5893 Remote Similarity NPC285594
0.5893 Remote Similarity NPC96551
0.5893 Remote Similarity NPC473494
0.5893 Remote Similarity NPC329550
0.5882 Remote Similarity NPC262968
0.5882 Remote Similarity NPC32603
0.5882 Remote Similarity NPC236623
0.587 Remote Similarity NPC208936
0.5862 Remote Similarity NPC288253
0.5854 Remote Similarity NPC12889
0.5849 Remote Similarity NPC100809
0.5849 Remote Similarity NPC209431
0.5849 Remote Similarity NPC63396
0.5849 Remote Similarity NPC202850
0.5833 Remote Similarity NPC129976
0.5833 Remote Similarity NPC88325
0.5818 Remote Similarity NPC193695
0.5818 Remote Similarity NPC192843
0.5814 Remote Similarity NPC279300
0.58 Remote Similarity NPC149821
0.58 Remote Similarity NPC5413
0.5789 Remote Similarity NPC25853
0.5778 Remote Similarity NPC101147
0.5778 Remote Similarity NPC323278
0.5769 Remote Similarity NPC161366
0.5769 Remote Similarity NPC281245
0.5769 Remote Similarity NPC92114
0.5769 Remote Similarity NPC473705
0.5741 Remote Similarity NPC188789
0.5714 Remote Similarity NPC22098
0.5714 Remote Similarity NPC94991
0.5714 Remote Similarity NPC195246
0.5714 Remote Similarity NPC308108
0.5714 Remote Similarity NPC266295
0.5714 Remote Similarity NPC276009
0.5714 Remote Similarity NPC170799
0.5714 Remote Similarity NPC33928
0.569 Remote Similarity NPC97322
0.569 Remote Similarity NPC475795
0.569 Remote Similarity NPC168407
0.5686 Remote Similarity NPC59051
0.5686 Remote Similarity NPC116906
0.5676 Remote Similarity NPC287191
0.5676 Remote Similarity NPC266539
0.5676 Remote Similarity NPC31891
0.5676 Remote Similarity NPC266144
0.5667 Remote Similarity NPC296436
0.5667 Remote Similarity NPC176215
0.5667 Remote Similarity NPC251118
0.566 Remote Similarity NPC14002
0.566 Remote Similarity NPC309606
0.566 Remote Similarity NPC39633
0.566 Remote Similarity NPC70387
0.566 Remote Similarity NPC294548
0.566 Remote Similarity NPC473784
0.566 Remote Similarity NPC1813
0.566 Remote Similarity NPC23117
0.566 Remote Similarity NPC321062
0.566 Remote Similarity NPC69898
0.566 Remote Similarity NPC36061
0.566 Remote Similarity NPC284224
0.566 Remote Similarity NPC139029
0.566 Remote Similarity NPC139545
0.566 Remote Similarity NPC295777
0.566 Remote Similarity NPC61177
0.5636 Remote Similarity NPC20603
0.5614 Remote Similarity NPC276764
0.5614 Remote Similarity NPC259261
0.5614 Remote Similarity NPC472304
0.5614 Remote Similarity NPC143834
0.561 Remote Similarity NPC266979
0.561 Remote Similarity NPC304788
0.56 Remote Similarity NPC207292
0.56 Remote Similarity NPC91495

  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 NPC220061 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
0.6279 Remote Similarity NPD5783 Phase 3
0.617 Remote Similarity NPD3174 Discontinued
0.5918 Remote Similarity NPD622 Approved
0.5882 Remote Similarity NPD29 Approved
0.5882 Remote Similarity NPD28 Approved
0.58 Remote Similarity NPD3173 Approved
0.5714 Remote Similarity NPD287 Approved
0.566 Remote Similarity NPD3172 Approved

  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