Structure

Physi-Chem Properties

Molecular Weight:  249.21
Volume:  288.613
LogP:  4.04
LogD:  3.512
LogS:  -3.424
# Rotatable Bonds:  9
TPSA:  20.31
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.469
Synthetic Accessibility Score:  2.444
Fsp3:  0.688
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.642
MDCK Permeability:  1.851374145189766e-05
Pgp-inhibitor:  0.781
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.871
30% Bioavailability (F30%):  0.726

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.975
Plasma Protein Binding (PPB):  93.99500274658203%
Volume Distribution (VD):  0.835
Pgp-substrate:  7.403360366821289%

ADMET: Metabolism

CYP1A2-inhibitor:  0.544
CYP1A2-substrate:  0.797
CYP2C19-inhibitor:  0.507
CYP2C19-substrate:  0.76
CYP2C9-inhibitor:  0.353
CYP2C9-substrate:  0.596
CYP2D6-inhibitor:  0.125
CYP2D6-substrate:  0.436
CYP3A4-inhibitor:  0.757
CYP3A4-substrate:  0.255

ADMET: Excretion

Clearance (CL):  5.859
Half-life (T1/2):  0.375

ADMET: Toxicity

hERG Blockers:  0.146
Human Hepatotoxicity (H-HT):  0.595
Drug-inuced Liver Injury (DILI):  0.019
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.506
Maximum Recommended Daily Dose:  0.718
Skin Sensitization:  0.981
Carcinogencity:  0.38
Eye Corrosion:  0.37
Eye Irritation:  0.68
Respiratory Toxicity:  0.943

Download Data

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

  Natural Product: NPC252684

Natural Product ID:  NPC252684
Common Name*:   1-(Pyrrolidin-1-Yl)Dodeca-2,4-Dien-1-One
IUPAC Name:   (2E,4E)-1-pyrrolidin-1-yldodeca-2,4-dien-1-one
Synonyms:  
Standard InCHIKey:  UAIYHWLHQSKQLW-PEGOPYGQSA-N
Standard InCHI:  InChI=1S/C16H27NO/c1-2-3-4-5-6-7-8-9-10-13-16(18)17-14-11-12-15-17/h8-10,13H,2-7,11-12,14-15H2,1H3/b9-8+,13-10+
SMILES:  CCCCCCC/C=C/C=C/C(=O)N1CCCC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3338739
PubChem CID:   10999431
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[571514]
NPT83 Cell Line MCF7 Homo sapiens IC50 > 40000.0 nM PMID[571514]
NPT133 Cell Line ZR-75-1 Homo sapiens IC50 > 40000.0 nM PMID[571514]
NPT134 Cell Line SK-BR-3 Homo sapiens IC50 > 40000.0 nM PMID[571514]
NPT82 Cell Line MDA-MB-231 Homo sapiens IC50 > 40000.0 nM PMID[571514]
NPT90 Cell Line DU-145 Homo sapiens IC50 > 40000.0 nM PMID[571514]
NPT91 Cell Line KB Homo sapiens IC50 > 40000.0 nM PMID[571514]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 40000.0 nM PMID[571514]

☑ 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 NPC252684 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
0.9649 High Similarity NPC133923
0.9474 High Similarity NPC385
0.871 High Similarity NPC206660
0.8525 High Similarity NPC42477
0.791 Intermediate Similarity NPC96272
0.726 Intermediate Similarity NPC34672
0.7143 Intermediate Similarity NPC226982
0.7143 Intermediate Similarity NPC277341
0.6875 Remote Similarity NPC475975
0.6795 Remote Similarity NPC209232
0.6494 Remote Similarity NPC320667
0.6494 Remote Similarity NPC214125
0.6486 Remote Similarity NPC97614
0.6456 Remote Similarity NPC471768
0.641 Remote Similarity NPC46268
0.641 Remote Similarity NPC25513
0.6364 Remote Similarity NPC63284
0.6265 Remote Similarity NPC143344
0.6265 Remote Similarity NPC61321
0.6265 Remote Similarity NPC234822
0.6265 Remote Similarity NPC135639
0.6265 Remote Similarity NPC78058
0.625 Remote Similarity NPC127430
0.625 Remote Similarity NPC120699
0.618 Remote Similarity NPC474974
0.6143 Remote Similarity NPC470738
0.6056 Remote Similarity NPC477459
0.6056 Remote Similarity NPC477461
0.6024 Remote Similarity NPC473810
0.6 Remote Similarity NPC86452
0.6 Remote Similarity NPC76283
0.6 Remote Similarity NPC244256
0.5949 Remote Similarity NPC281154
0.593 Remote Similarity NPC157479
0.5926 Remote Similarity NPC28529
0.5921 Remote Similarity NPC90782
0.5897 Remote Similarity NPC326126
0.5882 Remote Similarity NPC207048
0.5862 Remote Similarity NPC17497
0.5862 Remote Similarity NPC305602
0.5862 Remote Similarity NPC324506
0.5854 Remote Similarity NPC267203
0.5854 Remote Similarity NPC77890
0.5854 Remote Similarity NPC132858
0.5843 Remote Similarity NPC17143
0.5843 Remote Similarity NPC53240
0.5843 Remote Similarity NPC47230
0.5823 Remote Similarity NPC470994
0.5814 Remote Similarity NPC319913
0.5814 Remote Similarity NPC147513
0.5806 Remote Similarity NPC267514
0.5806 Remote Similarity NPC145755
0.5802 Remote Similarity NPC308050
0.5789 Remote Similarity NPC23721
0.5783 Remote Similarity NPC477523
0.5763 Remote Similarity NPC217923
0.5747 Remote Similarity NPC322672
0.5738 Remote Similarity NPC208936
0.5738 Remote Similarity NPC67920
0.5738 Remote Similarity NPC287397
0.5738 Remote Similarity NPC298710
0.573 Remote Similarity NPC81195
0.5714 Remote Similarity NPC477524
0.5714 Remote Similarity NPC477688
0.5714 Remote Similarity NPC473661
0.5714 Remote Similarity NPC143516
0.5696 Remote Similarity NPC252503
0.5682 Remote Similarity NPC473525
0.5658 Remote Similarity NPC76869
0.5658 Remote Similarity NPC477460
0.5657 Remote Similarity NPC474804
0.5657 Remote Similarity NPC474973
0.5657 Remote Similarity NPC130898
0.5652 Remote Similarity NPC273023
0.5647 Remote Similarity NPC215474
0.5641 Remote Similarity NPC328895
0.5638 Remote Similarity NPC52820

  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 NPC252684 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
0.5854 Remote Similarity NPD529 Approved
0.5769 Remote Similarity NPD816 Approved
0.5769 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