Structure

Physi-Chem Properties

Molecular Weight:  187.17
Volume:  203.364
LogP:  -1.327
LogD:  -1.79
LogS:  0.646
# Rotatable Bonds:  9
TPSA:  67.15
# H-Bond Aceptor:  4
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.463
Synthetic Accessibility Score:  2.026
Fsp3:  0.889
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:  -5.98
MDCK Permeability:  3.4924478313769214e-06
Pgp-inhibitor:  0.032
Pgp-substrate:  0.994
Human Intestinal Absorption (HIA):  0.135
20% Bioavailability (F20%):  0.036
30% Bioavailability (F30%):  0.052

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.388
Plasma Protein Binding (PPB):  21.58031463623047%
Volume Distribution (VD):  1.099
Pgp-substrate:  92.31745910644531%

ADMET: Metabolism

CYP1A2-inhibitor:  0.01
CYP1A2-substrate:  0.058
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.247
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.049
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.447
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.161

ADMET: Excretion

Clearance (CL):  4.819
Half-life (T1/2):  0.402

ADMET: Toxicity

hERG Blockers:  0.032
Human Hepatotoxicity (H-HT):  0.1
Drug-inuced Liver Injury (DILI):  0.032
AMES Toxicity:  0.156
Rat Oral Acute Toxicity:  0.092
Maximum Recommended Daily Dose:  0.039
Skin Sensitization:  0.765
Carcinogencity:  0.029
Eye Corrosion:  0.004
Eye Irritation:  0.051
Respiratory Toxicity:  0.62

Download Data

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

  Natural Product: NPC321202

Natural Product ID:  NPC321202
Common Name*:   N-[3-(4-Aminobutylamino)Propyl]Acetamide
IUPAC Name:   N-[3-(4-aminobutylamino)propyl]acetamide
Synonyms:  
Standard InCHIKey:  MQTAVJHICJWXBR-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H21N3O/c1-9(13)12-8-4-7-11-6-3-2-5-10/h11H,2-8,10H2,1H3,(H,12,13)
SMILES:  CC(=O)NCCCNCCCCN
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL176800
PubChem CID:   496
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0002285] Carboximidic acids and derivatives
        • [CHEMONTID:0002484] Carboximidic acids

*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

☑ 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
NPT5093 Individual Protein Polyamine oxidase Homo sapiens Ki = 1370000.0 nM PMID[489212]

☑ 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 NPC321202 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
0.9737 High Similarity NPC319114
0.8108 Intermediate Similarity NPC328698
0.7105 Intermediate Similarity NPC95589
0.7027 Intermediate Similarity NPC193536
0.7027 Intermediate Similarity NPC152949
0.7027 Intermediate Similarity NPC270175
0.6923 Remote Similarity NPC320889
0.6852 Remote Similarity NPC476537
0.6852 Remote Similarity NPC216415
0.6757 Remote Similarity NPC27675
0.6316 Remote Similarity NPC314510
0.6279 Remote Similarity NPC74599
0.6222 Remote Similarity NPC240230
0.6 Remote Similarity NPC326791
0.5962 Remote Similarity NPC110136
0.5814 Remote Similarity NPC328729
0.58 Remote Similarity NPC297220
0.5778 Remote Similarity NPC69179
0.575 Remote Similarity NPC232311
0.5738 Remote Similarity NPC262615
0.5676 Remote Similarity NPC119368
0.5652 Remote Similarity NPC473035
0.5636 Remote Similarity NPC321118
0.5636 Remote Similarity NPC316889

  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 NPC321202 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
0.8293 Intermediate Similarity NPD9227 Discontinued
0.7105 Intermediate Similarity NPD401 Approved
0.6923 Remote Similarity NPD1156 Clinical (unspecified phase)
0.6809 Remote Similarity NPD1154 Phase 3
0.6667 Remote Similarity NPD8613 Approved
0.6429 Remote Similarity NPD1155 Discontinued
0.6364 Remote Similarity NPD2707 Clinical (unspecified phase)
0.6341 Remote Similarity NPD2276 Clinical (unspecified phase)
0.6327 Remote Similarity NPD399 Approved
0.6327 Remote Similarity NPD400 Approved
0.6327 Remote Similarity NPD398 Approved
0.625 Remote Similarity NPD397 Phase 2
0.6087 Remote Similarity NPD2273 Clinical (unspecified phase)
0.5902 Remote Similarity NPD2703 Discontinued
0.5873 Remote Similarity NPD3213 Discontinued
0.5814 Remote Similarity NPD8556 Phase 3
0.575 Remote Similarity NPD9465 Approved
0.5745 Remote Similarity NPD1463 Clinical (unspecified phase)
0.5738 Remote Similarity NPD6438 Approved
0.5738 Remote Similarity NPD6437 Approved
0.5686 Remote Similarity NPD379 Clinical (unspecified phase)

  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