Structure

Physi-Chem Properties

Molecular Weight:  153.12
Volume:  176.098
LogP:  1.129
LogD:  0.765
LogS:  -1.383
# Rotatable Bonds:  4
TPSA:  43.09
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.613
Synthetic Accessibility Score:  3.168
Fsp3:  0.444
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.553
MDCK Permeability:  4.644008367904462e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.617
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.999
Plasma Protein Binding (PPB):  78.8618392944336%
Volume Distribution (VD):  1.007
Pgp-substrate:  24.240184783935547%

ADMET: Metabolism

CYP1A2-inhibitor:  0.087
CYP1A2-substrate:  0.1
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.356
CYP2C9-inhibitor:  0.011
CYP2C9-substrate:  0.189
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.3
CYP3A4-inhibitor:  0.034
CYP3A4-substrate:  0.273

ADMET: Excretion

Clearance (CL):  8.289
Half-life (T1/2):  0.354

ADMET: Toxicity

hERG Blockers:  0.058
Human Hepatotoxicity (H-HT):  0.456
Drug-inuced Liver Injury (DILI):  0.013
AMES Toxicity:  0.245
Rat Oral Acute Toxicity:  0.766
Maximum Recommended Daily Dose:  0.877
Skin Sensitization:  0.941
Carcinogencity:  0.776
Eye Corrosion:  0.013
Eye Irritation:  0.734
Respiratory Toxicity:  0.591

Download Data

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

  Natural Product: NPC91044

Natural Product ID:  NPC91044
Common Name*:   (2E,4E)-7-Methylocta-2,4-Dienamide
IUPAC Name:   (2E,4E)-7-methylocta-2,4-dienamide
Synonyms:  
Standard InCHIKey:  CMXDNZFOOPLNCF-BDWKERMESA-N
Standard InCHI:  InChI=1S/C9H15NO/c1-8(2)6-4-3-5-7-9(10)11/h3-5,7-8H,6H2,1-2H3,(H2,10,11)/b4-3+,7-5+
SMILES:  CC(C/C=C/C=C/C(=N)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL463899
PubChem CID:   16099485
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001093] Carboxylic acid derivatives
          • [CHEMONTID:0000475] Carboxylic acid amides
            • [CHEMONTID:0001662] Primary carboxylic acid amides

*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
NPO32837 streptomyces strain cnq-085 Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[17190455]

☑ 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
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 21.69 ug.mL-1 PMID[454502]

☑ 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 NPC91044 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
0.8462 Intermediate Similarity NPC4881
0.8367 Intermediate Similarity NPC307435
0.8367 Intermediate Similarity NPC267692
0.82 Intermediate Similarity NPC145032
0.82 Intermediate Similarity NPC243539
0.82 Intermediate Similarity NPC54542
0.82 Intermediate Similarity NPC304223
0.82 Intermediate Similarity NPC267340
0.8039 Intermediate Similarity NPC195986
0.7925 Intermediate Similarity NPC471992
0.7885 Intermediate Similarity NPC303672
0.7885 Intermediate Similarity NPC119655
0.7778 Intermediate Similarity NPC477049
0.7736 Intermediate Similarity NPC56028
0.7736 Intermediate Similarity NPC123669
0.7736 Intermediate Similarity NPC163912
0.7736 Intermediate Similarity NPC305288
0.7736 Intermediate Similarity NPC167759
0.7593 Intermediate Similarity NPC471991
0.7593 Intermediate Similarity NPC297020
0.7593 Intermediate Similarity NPC273023
0.7455 Intermediate Similarity NPC104138
0.7455 Intermediate Similarity NPC261158
0.7455 Intermediate Similarity NPC24216
0.7455 Intermediate Similarity NPC306420
0.7407 Intermediate Similarity NPC132669
0.7407 Intermediate Similarity NPC14234
0.7407 Intermediate Similarity NPC246519
0.7407 Intermediate Similarity NPC269800
0.7407 Intermediate Similarity NPC44193
0.7407 Intermediate Similarity NPC184014
0.7091 Intermediate Similarity NPC124382
0.7091 Intermediate Similarity NPC13011
0.7018 Intermediate Similarity NPC245650
0.6949 Remote Similarity NPC6795
0.678 Remote Similarity NPC312826
0.6471 Remote Similarity NPC86121
0.6452 Remote Similarity NPC471023
0.6452 Remote Similarity NPC77891
0.6406 Remote Similarity NPC187315
0.6349 Remote Similarity NPC253468
0.6349 Remote Similarity NPC235311
0.6346 Remote Similarity NPC138935
0.629 Remote Similarity NPC324077
0.6275 Remote Similarity NPC206906
0.625 Remote Similarity NPC477525
0.625 Remote Similarity NPC261571
0.623 Remote Similarity NPC74617
0.623 Remote Similarity NPC150505
0.6226 Remote Similarity NPC299114
0.62 Remote Similarity NPC56917
0.617 Remote Similarity NPC58957
0.6154 Remote Similarity NPC315141
0.6154 Remote Similarity NPC470439
0.6154 Remote Similarity NPC129995
0.614 Remote Similarity NPC49494
0.614 Remote Similarity NPC188341
0.614 Remote Similarity NPC208638
0.6136 Remote Similarity NPC32955
0.6032 Remote Similarity NPC273614
0.6027 Remote Similarity NPC314854
0.6027 Remote Similarity NPC313911
0.6 Remote Similarity NPC255042
0.6 Remote Similarity NPC29091
0.6 Remote Similarity NPC182840
0.6 Remote Similarity NPC15934
0.6 Remote Similarity NPC103213
0.5962 Remote Similarity NPC209279
0.5962 Remote Similarity NPC51758
0.5962 Remote Similarity NPC108494
0.5962 Remote Similarity NPC68889
0.5962 Remote Similarity NPC67761
0.5962 Remote Similarity NPC194586
0.5962 Remote Similarity NPC180871
0.5962 Remote Similarity NPC88079
0.5957 Remote Similarity NPC250734
0.5882 Remote Similarity NPC471022
0.5873 Remote Similarity NPC130807
0.5873 Remote Similarity NPC309877
0.5818 Remote Similarity NPC180575
0.5806 Remote Similarity NPC210999
0.5769 Remote Similarity NPC269823
0.566 Remote Similarity NPC304151
0.566 Remote Similarity NPC213538
0.566 Remote Similarity NPC256766
0.5634 Remote Similarity NPC314678

  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 NPC91044 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
0.5932 Remote Similarity NPD9652 Approved
0.5893 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