Structure

Physi-Chem Properties

Molecular Weight:  229.2
Volume:  235.925
LogP:  -2.437
LogD:  -1.973
LogS:  -1.21
# Rotatable Bonds:  10
TPSA:  138.33
# H-Bond Aceptor:  7
# H-Bond Donor:  9
# Rings:  0
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.162
Synthetic Accessibility Score:  2.515
Fsp3:  0.778
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -6.07
MDCK Permeability:  6.484980985987931e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.963
Human Intestinal Absorption (HIA):  0.027
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.961

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.509
Plasma Protein Binding (PPB):  15.892221450805664%
Volume Distribution (VD):  1.09
Pgp-substrate:  84.43569946289062%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.028
CYP2C19-inhibitor:  0.007
CYP2C19-substrate:  0.039
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.004
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.758
CYP3A4-inhibitor:  0.0
CYP3A4-substrate:  0.047

ADMET: Excretion

Clearance (CL):  5.356
Half-life (T1/2):  0.279

ADMET: Toxicity

hERG Blockers:  0.286
Human Hepatotoxicity (H-HT):  0.047
Drug-inuced Liver Injury (DILI):  0.016
AMES Toxicity:  0.055
Rat Oral Acute Toxicity:  0.204
Maximum Recommended Daily Dose:  0.101
Skin Sensitization:  0.803
Carcinogencity:  0.018
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.882

Download Data

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

  Natural Product: NPC240230

Natural Product ID:  NPC240230
Common Name*:   N-[4-(3-Guanidino-Propylamino)-Butyl]-Guanidine
IUPAC Name:   2-[3-[4-(diaminomethylideneamino)butylamino]propyl]guanidine
Synonyms:  
Standard InCHIKey:  KESWKVCUKVUPPR-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H23N7/c10-8(11)15-6-2-1-4-14-5-3-7-16-9(12)13/h14H,1-7H2,(H4,10,11,15)(H4,12,13,16)
SMILES:  C(CCNC(=N)N)CNCCCNC(=N)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL67661
PubChem CID:   159662
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
NPO15396 Neptunia oleracea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14877 Alstonia verticillosa Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8488 Cissampelos insularis Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3398 Solanum kieseritzkii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12426 Lycoris albiflora Species Amaryllidaceae 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
NPT12 Individual Protein Human immunodeficiency virus type 1 integrase Human immunodeficiency virus 1 Inhibition < 50.0 % PMID[480899]

☑ 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 NPC240230 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
0.8889 High Similarity NPC163099
0.8684 High Similarity NPC270319
0.7778 Intermediate Similarity NPC95589
0.7234 Intermediate Similarity NPC32934
0.7222 Intermediate Similarity NPC152949
0.7222 Intermediate Similarity NPC193536
0.7105 Intermediate Similarity NPC320889
0.6944 Remote Similarity NPC27675
0.6829 Remote Similarity NPC74599
0.6757 Remote Similarity NPC270175
0.6596 Remote Similarity NPC188989
0.6444 Remote Similarity NPC319114
0.6304 Remote Similarity NPC97568
0.6304 Remote Similarity NPC253366
0.6222 Remote Similarity NPC321202
0.617 Remote Similarity NPC223653
0.6136 Remote Similarity NPC326791
0.5962 Remote Similarity NPC153280
0.5897 Remote Similarity NPC232311
0.5849 Remote Similarity NPC245768
0.5769 Remote Similarity NPC110136
0.561 Remote Similarity NPC21157

  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 NPC240230 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
0.8421 Intermediate Similarity NPD9059 Approved
0.8293 Intermediate Similarity NPD9458 Approved
0.7778 Intermediate Similarity NPD401 Approved
0.7609 Intermediate Similarity NPD395 Approved
0.7609 Intermediate Similarity NPD396 Approved
0.7105 Intermediate Similarity NPD1156 Clinical (unspecified phase)
0.6923 Remote Similarity NPD2276 Clinical (unspecified phase)
0.6591 Remote Similarity NPD9015 Phase 2
0.6545 Remote Similarity NPD1155 Discontinued
0.6512 Remote Similarity NPD2707 Clinical (unspecified phase)
0.6316 Remote Similarity NPD9465 Approved
0.6222 Remote Similarity NPD2273 Clinical (unspecified phase)
0.6053 Remote Similarity NPD9063 Approved
0.6053 Remote Similarity NPD9064 Approved
0.6 Remote Similarity NPD2703 Discontinued
0.587 Remote Similarity NPD1463 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3213 Discontinued
0.5625 Remote Similarity NPD2702 Phase 1
0.5625 Remote Similarity NPD2704 Phase 3
0.56 Remote Similarity NPD8792 Approved
0.56 Remote Similarity NPD1154 Phase 3
0.56 Remote Similarity NPD8793 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