Structure

Physi-Chem Properties

Molecular Weight:  245.18
Volume:  289.26
LogP:  3.109
LogD:  3.142
LogS:  -2.799
# 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:  0.565
Synthetic Accessibility Score:  3.483
Fsp3:  0.438
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -3.976
MDCK Permeability:  5.379991125664674e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.638

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.972
Plasma Protein Binding (PPB):  97.65167999267578%
Volume Distribution (VD):  0.97
Pgp-substrate:  1.5424816608428955%

ADMET: Metabolism

CYP1A2-inhibitor:  0.893
CYP1A2-substrate:  0.247
CYP2C19-inhibitor:  0.955
CYP2C19-substrate:  0.652
CYP2C9-inhibitor:  0.815
CYP2C9-substrate:  0.214
CYP2D6-inhibitor:  0.265
CYP2D6-substrate:  0.266
CYP3A4-inhibitor:  0.863
CYP3A4-substrate:  0.27

ADMET: Excretion

Clearance (CL):  11.998
Half-life (T1/2):  0.814

ADMET: Toxicity

hERG Blockers:  0.077
Human Hepatotoxicity (H-HT):  0.852
Drug-inuced Liver Injury (DILI):  0.255
AMES Toxicity:  0.126
Rat Oral Acute Toxicity:  0.803
Maximum Recommended Daily Dose:  0.903
Skin Sensitization:  0.968
Carcinogencity:  0.897
Eye Corrosion:  0.063
Eye Irritation:  0.796
Respiratory Toxicity:  0.91

Download Data

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

  Natural Product: NPC305288

Natural Product ID:  NPC305288
Common Name*:   Dodeca-2Z, 4E, 10Z-Trien-8-Ynoic Acid Isobutylamide
IUPAC Name:   (2Z,4E,10Z)-N-(2-methylpropyl)dodeca-2,4,10-trien-8-ynamide
Synonyms:  
Standard InCHIKey:  NFFPFDVUIWBNTI-GBEDUDKYSA-N
Standard InCHI:  InChI=1S/C16H23NO/c1-4-5-6-7-8-9-10-11-12-13-16(18)17-14-15(2)3/h4-5,10-13,15H,8-9,14H2,1-3H3,(H,17,18)/b5-4-,11-10+,13-12-
SMILES:  C/C=CC#CCC/C=C/C=CC(=NCC(C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL456939
PubChem CID:   5326171
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
NPO726 Echinacea angustifolia Species Asteraceae Eukaryota root n.a. n.a. PMID[15921428]
NPO726 Echinacea angustifolia 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 TD50 = 30.0 ug ml-1 PMID[543680]
NPT113 Cell Line RAW264.7 Mus musculus ID50 = 12.0 ug ml-1 PMID[543680]

☑ 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 NPC305288 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
1.0 High Similarity NPC163912
1.0 High Similarity NPC167759
1.0 High Similarity NPC56028
0.9804 High Similarity NPC471991
0.98 High Similarity NPC119655
0.9615 High Similarity NPC477049
0.9608 High Similarity NPC123669
0.94 High Similarity NPC243539
0.94 High Similarity NPC54542
0.94 High Similarity NPC145032
0.94 High Similarity NPC304223
0.94 High Similarity NPC267340
0.92 High Similarity NPC267692
0.92 High Similarity NPC307435
0.9038 High Similarity NPC303672
0.8868 High Similarity NPC13011
0.8868 High Similarity NPC124382
0.8846 High Similarity NPC195986
0.8704 High Similarity NPC273023
0.8704 High Similarity NPC471992
0.8704 High Similarity NPC297020
0.8545 High Similarity NPC104138
0.8545 High Similarity NPC261158
0.8545 High Similarity NPC24216
0.8545 High Similarity NPC306420
0.8519 High Similarity NPC246519
0.8519 High Similarity NPC14234
0.8519 High Similarity NPC269800
0.8519 High Similarity NPC184014
0.8519 High Similarity NPC44193
0.8519 High Similarity NPC132669
0.7966 Intermediate Similarity NPC6795
0.7797 Intermediate Similarity NPC312826
0.7759 Intermediate Similarity NPC245650
0.7736 Intermediate Similarity NPC91044
0.7667 Intermediate Similarity NPC309877
0.7419 Intermediate Similarity NPC471023
0.7344 Intermediate Similarity NPC187315
0.7302 Intermediate Similarity NPC235311
0.7302 Intermediate Similarity NPC253468
0.7213 Intermediate Similarity NPC150505
0.7213 Intermediate Similarity NPC74617
0.7188 Intermediate Similarity NPC477525
0.7143 Intermediate Similarity NPC77891
0.7077 Intermediate Similarity NPC129995
0.7077 Intermediate Similarity NPC315141
0.7 Intermediate Similarity NPC4881
0.6984 Remote Similarity NPC324077
0.6981 Remote Similarity NPC86121
0.6981 Remote Similarity NPC470439
0.6825 Remote Similarity NPC130807
0.6765 Remote Similarity NPC471022
0.6719 Remote Similarity NPC273614
0.6607 Remote Similarity NPC180575
0.6508 Remote Similarity NPC210999
0.6481 Remote Similarity NPC206906
0.6479 Remote Similarity NPC314678
0.6462 Remote Similarity NPC29468
0.6429 Remote Similarity NPC299114
0.6364 Remote Similarity NPC182758
0.629 Remote Similarity NPC242930
0.6271 Remote Similarity NPC291437
0.6271 Remote Similarity NPC328784
0.625 Remote Similarity NPC138935
0.6182 Remote Similarity NPC304151
0.6143 Remote Similarity NPC249713
0.614 Remote Similarity NPC269074
0.6 Remote Similarity NPC321030
0.6 Remote Similarity NPC325734
0.5949 Remote Similarity NPC14326
0.5909 Remote Similarity NPC329003
0.5909 Remote Similarity NPC325550
0.5909 Remote Similarity NPC326524
0.5902 Remote Similarity NPC71053
0.5902 Remote Similarity NPC59408
0.5873 Remote Similarity NPC110732
0.5862 Remote Similarity NPC276825
0.5833 Remote Similarity NPC291196
0.5833 Remote Similarity NPC103712
0.5833 Remote Similarity NPC31194
0.5833 Remote Similarity NPC85079
0.5833 Remote Similarity NPC248884
0.5833 Remote Similarity NPC45060
0.5833 Remote Similarity NPC153538
0.5833 Remote Similarity NPC280065
0.5806 Remote Similarity NPC208638
0.5781 Remote Similarity NPC474644
0.5769 Remote Similarity NPC314854
0.5769 Remote Similarity NPC313911
0.5763 Remote Similarity NPC124183
0.5763 Remote Similarity NPC55063
0.5763 Remote Similarity NPC19834
0.5763 Remote Similarity NPC35141
0.5738 Remote Similarity NPC249670
0.5738 Remote Similarity NPC72699
0.5738 Remote Similarity NPC473913
0.5738 Remote Similarity NPC474642
0.5714 Remote Similarity NPC269823
0.5714 Remote Similarity NPC61177
0.5714 Remote Similarity NPC34577
0.5692 Remote Similarity NPC474643
0.5692 Remote Similarity NPC473865
0.569 Remote Similarity NPC101616
0.5652 Remote Similarity NPC477106
0.5652 Remote Similarity NPC316674
0.5645 Remote Similarity NPC151782
0.5645 Remote Similarity NPC93639
0.5645 Remote Similarity NPC261571
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
0.5614 Remote Similarity NPC213538
0.5614 Remote Similarity NPC256766
0.5606 Remote Similarity NPC472445

  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 NPC305288 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
0.5833 Remote Similarity NPD4220 Pre-registration

  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