Structure

Physi-Chem Properties

Molecular Weight:  247.19
Volume:  285.977
LogP:  3.184
LogD:  3.396
LogS:  -3.571
# Rotatable Bonds:  8
TPSA:  20.31
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.38
Synthetic Accessibility Score:  2.53
Fsp3:  0.562
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.705
MDCK Permeability:  3.412266232771799e-05
Pgp-inhibitor:  0.707
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.073
30% Bioavailability (F30%):  0.915

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.585
Plasma Protein Binding (PPB):  89.3808822631836%
Volume Distribution (VD):  0.463
Pgp-substrate:  8.606476783752441%

ADMET: Metabolism

CYP1A2-inhibitor:  0.637
CYP1A2-substrate:  0.737
CYP2C19-inhibitor:  0.873
CYP2C19-substrate:  0.726
CYP2C9-inhibitor:  0.43
CYP2C9-substrate:  0.988
CYP2D6-inhibitor:  0.868
CYP2D6-substrate:  0.931
CYP3A4-inhibitor:  0.769
CYP3A4-substrate:  0.146

ADMET: Excretion

Clearance (CL):  2.713
Half-life (T1/2):  0.215

ADMET: Toxicity

hERG Blockers:  0.883
Human Hepatotoxicity (H-HT):  0.144
Drug-inuced Liver Injury (DILI):  0.232
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.046
Maximum Recommended Daily Dose:  0.062
Skin Sensitization:  0.947
Carcinogencity:  0.264
Eye Corrosion:  0.942
Eye Irritation:  0.981
Respiratory Toxicity:  0.946

Download Data

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

  Natural Product: NPC133923

Natural Product ID:  NPC133923
Common Name*:   1-(Pyrrolidin-1-Yl)Dodeca-2,4,6-Trien-1-One
IUPAC Name:   (2E,4E,6E)-1-pyrrolidin-1-yldodeca-2,4,6-trien-1-one
Synonyms:  
Standard InCHIKey:  JWOSQNYJGWMFTO-NRWMFWRASA-N
Standard InCHI:  InChI=1S/C16H25NO/c1-2-3-4-5-6-7-8-9-10-13-16(18)17-14-11-12-15-17/h6-10,13H,2-5,11-12,14-15H2,1H3/b7-6+,9-8+,13-10+
SMILES:  CCCCC/C=C/C=C/C=C/C(=O)N1CCCC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1669584
PubChem CID:   50994143
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines
        • [CHEMONTID:0003023] N-acylpyrrolidines

*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
NPO30128 Piper boehmeriaefolium Species Piperaceae Eukaryota whole plant Luxi County, Yunnan Province, China 2008-OCT PMID[21158422]
NPO30128 Piper boehmeriaefolium Species Piperaceae Eukaryota n.a. whole plant n.a. PMID[21158422]
NPO30128 Piper boehmeriaefolium Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]

☑ 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
NPT81 Cell Line A549 Homo sapiens IC50 > 40000.0 nM PMID[481651]
NPT83 Cell Line MCF7 Homo sapiens IC50 > 40000.0 nM PMID[481651]
NPT133 Cell Line ZR-75-1 Homo sapiens IC50 > 40000.0 nM PMID[481651]
NPT134 Cell Line SK-BR-3 Homo sapiens IC50 > 40000.0 nM PMID[481651]
NPT82 Cell Line MDA-MB-231 Homo sapiens IC50 > 40000.0 nM PMID[481651]
NPT90 Cell Line DU-145 Homo sapiens IC50 > 40000.0 nM PMID[481651]
NPT91 Cell Line KB Homo sapiens IC50 > 40000.0 nM PMID[481651]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 40000.0 nM PMID[481651]

☑ 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 NPC133923 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
0.9818 High Similarity NPC385
0.9649 High Similarity NPC252684
0.8814 High Similarity NPC42477
0.8387 Intermediate Similarity NPC206660
0.8154 Intermediate Similarity NPC96272
0.7333 Intermediate Similarity NPC277341
0.7333 Intermediate Similarity NPC226982
0.7051 Intermediate Similarity NPC475975
0.6986 Remote Similarity NPC34672
0.6667 Remote Similarity NPC320667
0.6667 Remote Similarity NPC214125
0.6623 Remote Similarity NPC471768
0.6579 Remote Similarity NPC25513
0.6538 Remote Similarity NPC209232
0.6533 Remote Similarity NPC63284
0.6324 Remote Similarity NPC470738
0.6216 Remote Similarity NPC97614
0.6154 Remote Similarity NPC46268
0.6154 Remote Similarity NPC86452
0.6154 Remote Similarity NPC244256
0.6136 Remote Similarity NPC474974
0.6081 Remote Similarity NPC90782
0.6053 Remote Similarity NPC326126
0.6024 Remote Similarity NPC135639
0.6024 Remote Similarity NPC78058
0.6024 Remote Similarity NPC143344
0.6024 Remote Similarity NPC234822
0.6024 Remote Similarity NPC61321
0.6 Remote Similarity NPC132858
0.6 Remote Similarity NPC127430
0.6 Remote Similarity NPC77890
0.6 Remote Similarity NPC120699
0.6 Remote Similarity NPC267203
0.5932 Remote Similarity NPC208936
0.5875 Remote Similarity NPC28529
0.5867 Remote Similarity NPC477688
0.5844 Remote Similarity NPC252503
0.5814 Remote Similarity NPC17497
0.5814 Remote Similarity NPC305602
0.5783 Remote Similarity NPC473810
0.5775 Remote Similarity NPC477461
0.5775 Remote Similarity NPC477459
0.5769 Remote Similarity NPC470994
0.5765 Remote Similarity NPC76283
0.5733 Remote Similarity NPC23721
0.5698 Remote Similarity NPC157479
0.5698 Remote Similarity NPC469860
0.5698 Remote Similarity NPC130436
0.5698 Remote Similarity NPC469861
0.5696 Remote Similarity NPC281154
0.569 Remote Similarity NPC217923
0.567 Remote Similarity NPC143516
0.5647 Remote Similarity NPC207048
0.5632 Remote Similarity NPC324506
0.5618 Remote Similarity NPC47230
0.5618 Remote Similarity NPC53240
0.5618 Remote Similarity NPC17143
0.5612 Remote Similarity NPC130898
0.5612 Remote Similarity NPC474973
0.5612 Remote Similarity NPC474804

  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 NPC133923 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
0.6 Remote Similarity NPD529 Approved
0.5714 Remote Similarity NPD816 Approved
0.5714 Remote Similarity NPD815 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