Structure

Physi-Chem Properties

Molecular Weight:  229.15
Volume:  269.328
LogP:  2.69
LogD:  2.506
LogS:  -2.688
# Rotatable Bonds:  7
TPSA:  29.1
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.549
Synthetic Accessibility Score:  3.468
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -3.813
MDCK Permeability:  6.58784992992878e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.079
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.542

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.516
Plasma Protein Binding (PPB):  96.34896087646484%
Volume Distribution (VD):  0.84
Pgp-substrate:  1.659489631652832%

ADMET: Metabolism

CYP1A2-inhibitor:  0.921
CYP1A2-substrate:  0.229
CYP2C19-inhibitor:  0.961
CYP2C19-substrate:  0.548
CYP2C9-inhibitor:  0.866
CYP2C9-substrate:  0.912
CYP2D6-inhibitor:  0.407
CYP2D6-substrate:  0.807
CYP3A4-inhibitor:  0.81
CYP3A4-substrate:  0.228

ADMET: Excretion

Clearance (CL):  10.26
Half-life (T1/2):  0.729

ADMET: Toxicity

hERG Blockers:  0.082
Human Hepatotoxicity (H-HT):  0.818
Drug-inuced Liver Injury (DILI):  0.415
AMES Toxicity:  0.271
Rat Oral Acute Toxicity:  0.937
Maximum Recommended Daily Dose:  0.878
Skin Sensitization:  0.969
Carcinogencity:  0.898
Eye Corrosion:  0.133
Eye Irritation:  0.76
Respiratory Toxicity:  0.958

Download Data

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

  Natural Product: NPC123669

Natural Product ID:  NPC123669
Common Name*:   Undeca-2Z,4E-Diene-8,10-Diynoic Acid Isobutylamide
IUPAC Name:   (2Z,4E)-N-(2-methylpropyl)undeca-2,4-dien-8,10-diynamide
Synonyms:  
Standard InCHIKey:  PSAKYIJFKFCZFO-PVHUKWJHSA-N
Standard InCHI:  InChI=1S/C15H19NO/c1-4-5-6-7-8-9-10-11-12-15(17)16-13-14(2)3/h1,9-12,14H,7-8,13H2,2-3H3,(H,16,17)/b10-9+,12-11-
SMILES:  C#CC#CCC/C=C/C=CC(=NCC(C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL464984
PubChem CID:   15609885
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000331] Fatty amides
          • [CHEMONTID:0001096] N-acyl amines

*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
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota root n.a. n.a. PMID[15921428]
NPO726 Echinacea angustifolia Species Asteraceae Eukaryota root n.a. n.a. PMID[15921428]
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota flowers n.a. n.a. PMID[19374389]
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14484 Echinacea purpurea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO726 Echinacea angustifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14484 Echinacea purpurea 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
NPT113 Cell Line RAW264.7 Mus musculus ID50 = 12.5 ug ml-1 PMID[502933]
NPT113 Cell Line RAW264.7 Mus musculus TD50 = 50.0 ug ml-1 PMID[502933]

☑ 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 NPC123669 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
0.9608 High Similarity NPC167759
0.9608 High Similarity NPC163912
0.9608 High Similarity NPC305288
0.9608 High Similarity NPC56028
0.9423 High Similarity NPC471991
0.9412 High Similarity NPC119655
0.9245 High Similarity NPC477049
0.9231 High Similarity NPC13011
0.9231 High Similarity NPC124382
0.92 High Similarity NPC267692
0.92 High Similarity NPC307435
0.902 High Similarity NPC267340
0.902 High Similarity NPC54542
0.902 High Similarity NPC145032
0.902 High Similarity NPC304223
0.902 High Similarity NPC243539
0.8846 High Similarity NPC195986
0.8679 High Similarity NPC303672
0.8364 Intermediate Similarity NPC471992
0.8364 Intermediate Similarity NPC297020
0.8364 Intermediate Similarity NPC273023
0.8214 Intermediate Similarity NPC261158
0.8214 Intermediate Similarity NPC306420
0.8214 Intermediate Similarity NPC24216
0.8214 Intermediate Similarity NPC104138
0.8182 Intermediate Similarity NPC132669
0.8182 Intermediate Similarity NPC14234
0.8182 Intermediate Similarity NPC246519
0.8182 Intermediate Similarity NPC44193
0.8182 Intermediate Similarity NPC184014
0.8182 Intermediate Similarity NPC269800
0.7759 Intermediate Similarity NPC245650
0.7736 Intermediate Similarity NPC91044
0.7667 Intermediate Similarity NPC6795
0.75 Intermediate Similarity NPC312826
0.7377 Intermediate Similarity NPC309877
0.7143 Intermediate Similarity NPC471023
0.7143 Intermediate Similarity NPC77891
0.7077 Intermediate Similarity NPC187315
0.7031 Intermediate Similarity NPC235311
0.7031 Intermediate Similarity NPC253468
0.7 Intermediate Similarity NPC4881
0.6984 Remote Similarity NPC324077
0.6981 Remote Similarity NPC86121
0.6981 Remote Similarity NPC470439
0.6935 Remote Similarity NPC74617
0.6935 Remote Similarity NPC150505
0.6923 Remote Similarity NPC477525
0.6818 Remote Similarity NPC129995
0.6818 Remote Similarity NPC315141
0.6719 Remote Similarity NPC273614
0.6562 Remote Similarity NPC130807
0.6522 Remote Similarity NPC471022
0.6481 Remote Similarity NPC206906
0.6429 Remote Similarity NPC299114
0.6316 Remote Similarity NPC180575
0.625 Remote Similarity NPC210999
0.625 Remote Similarity NPC314678
0.6212 Remote Similarity NPC29468
0.6182 Remote Similarity NPC304151
0.6119 Remote Similarity NPC182758
0.6032 Remote Similarity NPC242930
0.6 Remote Similarity NPC291437
0.6 Remote Similarity NPC328784
0.5965 Remote Similarity NPC138935
0.5915 Remote Similarity NPC249713
0.5862 Remote Similarity NPC269074
0.5781 Remote Similarity NPC474644
0.5758 Remote Similarity NPC321030
0.5758 Remote Similarity NPC325734
0.575 Remote Similarity NPC14326
0.5738 Remote Similarity NPC249670
0.5738 Remote Similarity NPC473913
0.5738 Remote Similarity NPC474642
0.5692 Remote Similarity NPC474643
0.5692 Remote Similarity NPC473865
0.5672 Remote Similarity NPC325550
0.5672 Remote Similarity NPC329003
0.5672 Remote Similarity NPC326524
0.5645 Remote Similarity NPC59408
0.5645 Remote Similarity NPC71053
0.5636 Remote Similarity NPC103213
0.5636 Remote Similarity NPC255042
0.5636 Remote Similarity NPC29091
0.5636 Remote Similarity NPC15934
0.5636 Remote Similarity NPC182840
0.5625 Remote Similarity NPC110732
0.5616 Remote Similarity NPC103712
0.5616 Remote Similarity NPC291196
0.5616 Remote Similarity NPC280065
0.5616 Remote Similarity NPC45060

  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 NPC123669 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
0.614 Remote Similarity NPD860 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