Structure

Physi-Chem Properties

Molecular Weight:  155.13
Volume:  178.734
LogP:  1.72
LogD:  1.622
LogS:  -1.17
# Rotatable Bonds:  4
TPSA:  29.1
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.618
Synthetic Accessibility Score:  2.392
Fsp3:  0.667
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:  -4.268
MDCK Permeability:  2.7753600079449825e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.013
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.057
30% Bioavailability (F30%):  0.013

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.914
Plasma Protein Binding (PPB):  61.12187194824219%
Volume Distribution (VD):  1.141
Pgp-substrate:  50.24086380004883%

ADMET: Metabolism

CYP1A2-inhibitor:  0.88
CYP1A2-substrate:  0.583
CYP2C19-inhibitor:  0.505
CYP2C19-substrate:  0.88
CYP2C9-inhibitor:  0.211
CYP2C9-substrate:  0.683
CYP2D6-inhibitor:  0.026
CYP2D6-substrate:  0.623
CYP3A4-inhibitor:  0.024
CYP3A4-substrate:  0.242

ADMET: Excretion

Clearance (CL):  8.353
Half-life (T1/2):  0.818

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.145
Drug-inuced Liver Injury (DILI):  0.042
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.072
Maximum Recommended Daily Dose:  0.021
Skin Sensitization:  0.245
Carcinogencity:  0.115
Eye Corrosion:  0.142
Eye Irritation:  0.966
Respiratory Toxicity:  0.091

Download Data

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

  Natural Product: NPC470439

Natural Product ID:  NPC470439
Common Name*:   N-2-Methylpropyl-2-Methylbutenamide
IUPAC Name:   (E)-2-methyl-N-(2-methylpropyl)but-2-enamide
Synonyms:  
Standard InCHIKey:  RPFDZLFZNNCJEC-VMPITWQZSA-N
Standard InCHI:  InChI=1S/C9H17NO/c1-5-8(4)9(11)10-6-7(2)3/h5,7H,6H2,1-4H3,(H,10,11)/b8-5+
SMILES:  C/C=C(/C(=NCC(C)C)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2036491
PubChem CID:   57408889
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
NPO24024 Fusarium semitectum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[10978211]
NPO24024 Fusarium semitectum Species Nectriaceae Eukaryota n.a. n.a. n.a. PMID[22439674]
NPO24024 Fusarium semitectum Species Nectriaceae 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
NPT111 Cell Line K562 Homo sapiens GI50 > 300000.0 nM PMID[458704]
NPT737 Cell Line HUVEC Homo sapiens GI50 > 300000.0 nM PMID[458704]
NPT165 Cell Line HeLa Homo sapiens CC50 > 300000.0 nM PMID[458704]

☑ 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 NPC470439 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
0.7551 Intermediate Similarity NPC307435
0.7551 Intermediate Similarity NPC267692
0.74 Intermediate Similarity NPC267340
0.74 Intermediate Similarity NPC145032
0.74 Intermediate Similarity NPC54542
0.74 Intermediate Similarity NPC243539
0.74 Intermediate Similarity NPC304223
0.7255 Intermediate Similarity NPC195986
0.7115 Intermediate Similarity NPC119655
0.7115 Intermediate Similarity NPC303672
0.6981 Remote Similarity NPC167759
0.6981 Remote Similarity NPC13011
0.6981 Remote Similarity NPC56028
0.6981 Remote Similarity NPC124382
0.6981 Remote Similarity NPC305288
0.6981 Remote Similarity NPC163912
0.6981 Remote Similarity NPC123669
0.6852 Remote Similarity NPC471992
0.6852 Remote Similarity NPC471991
0.6852 Remote Similarity NPC273023
0.6852 Remote Similarity NPC297020
0.6842 Remote Similarity NPC130807
0.6727 Remote Similarity NPC477049
0.6727 Remote Similarity NPC261158
0.6727 Remote Similarity NPC24216
0.6727 Remote Similarity NPC306420
0.6727 Remote Similarity NPC104138
0.6724 Remote Similarity NPC29468
0.6667 Remote Similarity NPC44193
0.6667 Remote Similarity NPC246519
0.6667 Remote Similarity NPC184014
0.6667 Remote Similarity NPC132669
0.6667 Remote Similarity NPC14234
0.6667 Remote Similarity NPC269800
0.6607 Remote Similarity NPC245650
0.6327 Remote Similarity NPC86121
0.6271 Remote Similarity NPC6795
0.6271 Remote Similarity NPC309877
0.6207 Remote Similarity NPC210999
0.6167 Remote Similarity NPC273614
0.6154 Remote Similarity NPC91044
0.6129 Remote Similarity NPC477525
0.6102 Remote Similarity NPC312826
0.6102 Remote Similarity NPC150505
0.6102 Remote Similarity NPC74617
0.6094 Remote Similarity NPC249713
0.6066 Remote Similarity NPC471023
0.6042 Remote Similarity NPC145077
0.6032 Remote Similarity NPC315141
0.6032 Remote Similarity NPC129995
0.6 Remote Similarity NPC280065
0.6 Remote Similarity NPC45060
0.5968 Remote Similarity NPC235311
0.5968 Remote Similarity NPC253468
0.5862 Remote Similarity NPC4881
0.5814 Remote Similarity NPC242117
0.5806 Remote Similarity NPC77891
0.5781 Remote Similarity NPC187315
0.569 Remote Similarity NPC242930
0.566 Remote Similarity NPC282097
0.5645 Remote Similarity NPC324077

  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 NPC470439 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
0.5769 Remote Similarity NPD860 Phase 2
0.5667 Remote Similarity NPD9368 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