Structure

Physi-Chem Properties

Molecular Weight:  198.18
Volume:  220.23
LogP:  0.934
LogD:  -0.96
LogS:  -0.172
# Rotatable Bonds:  7
TPSA:  76.43
# H-Bond Aceptor:  4
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.253
Synthetic Accessibility Score:  2.848
Fsp3:  0.7
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:  -5.873
MDCK Permeability:  6.826603566878475e-06
Pgp-inhibitor:  0.003
Pgp-substrate:  0.997
Human Intestinal Absorption (HIA):  0.015
20% Bioavailability (F20%):  0.046
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.659
Plasma Protein Binding (PPB):  20.873741149902344%
Volume Distribution (VD):  1.456
Pgp-substrate:  78.87464141845703%

ADMET: Metabolism

CYP1A2-inhibitor:  0.04
CYP1A2-substrate:  0.079
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.096
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.075
CYP2D6-inhibitor:  0.665
CYP2D6-substrate:  0.855
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.164

ADMET: Excretion

Clearance (CL):  11.495
Half-life (T1/2):  0.387

ADMET: Toxicity

hERG Blockers:  0.12
Human Hepatotoxicity (H-HT):  0.183
Drug-inuced Liver Injury (DILI):  0.022
AMES Toxicity:  0.069
Rat Oral Acute Toxicity:  0.808
Maximum Recommended Daily Dose:  0.093
Skin Sensitization:  0.651
Carcinogencity:  0.054
Eye Corrosion:  0.003
Eye Irritation:  0.019
Respiratory Toxicity:  0.948

Download Data

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

  Natural Product: NPC32934

Natural Product ID:  NPC32934
Common Name*:   N-Prenyl Agmatine
IUPAC Name:   1-(4-aminobutyl)-2-(3-methylbut-2-enyl)guanidine
Synonyms:   N-Prenyl Agmatine
Standard InCHIKey:  VACJHYSOFQSYAC-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H22N4/c1-9(2)5-8-14-10(12)13-7-4-3-6-11/h5H,3-4,6-8,11H2,1-2H3,(H3,12,13,14)
SMILES:  NCCCCNC(=N)NCC=C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL111759
PubChem CID:   10081459
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0000375] Guanidines

*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
NPO32747 verbesina caracasana Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[10576697]
NPO32747 verbesina caracasana Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[8411013]

☑ 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
NPT4888 Individual Protein Polyamine oxidase Zea mays Ki = 15.0 nM PMID[528133]
NPT29 Organism Rattus norvegicus Rattus norvegicus Change = -11.0 % PMID[528131]
NPT29 Organism Rattus norvegicus Rattus norvegicus Change = -17.0 % PMID[528131]
NPT29 Organism Rattus norvegicus Rattus norvegicus Change = -4.0 % PMID[528131]
NPT29 Organism Rattus norvegicus Rattus norvegicus Change = 23.0 % PMID[528131]
NPT29 Organism Rattus norvegicus Rattus norvegicus Change = 4.0 % PMID[528131]
NPT29 Organism Rattus norvegicus Rattus norvegicus Change = 11.0 % PMID[528131]
NPT32 Organism Mus musculus Mus musculus Activity = -11.0 % PMID[528132]
NPT32 Organism Mus musculus Mus musculus Activity = -13.0 % PMID[528132]
NPT32 Organism Mus musculus Mus musculus Activity = -37.0 % PMID[528132]
NPT32 Organism Mus musculus Mus musculus Activity = -53.0 % PMID[528132]

☑ 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 NPC32934 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
0.9333 High Similarity NPC188989
0.8667 High Similarity NPC253366
0.8667 High Similarity NPC97568
0.8085 Intermediate Similarity NPC223653
0.8039 Intermediate Similarity NPC153280
0.7333 Intermediate Similarity NPC325268
0.7234 Intermediate Similarity NPC240230
0.7111 Intermediate Similarity NPC163099
0.7021 Intermediate Similarity NPC270319
0.6786 Remote Similarity NPC39250
0.625 Remote Similarity NPC230087

  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 NPC32934 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
0.7556 Intermediate Similarity NPD9059 Approved
0.75 Intermediate Similarity NPD9458 Approved
0.6735 Remote Similarity NPD1463 Clinical (unspecified phase)
0.6226 Remote Similarity NPD9675 Approved
0.6226 Remote Similarity NPD9674 Approved
0.6087 Remote Similarity NPD1144 Phase 2
0.6078 Remote Similarity NPD9015 Phase 2
0.6071 Remote Similarity NPD396 Approved
0.6071 Remote Similarity NPD395 Approved
0.5758 Remote Similarity NPD1098 Approved
0.5758 Remote Similarity NPD1097 Approved

  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