Structure

Physi-Chem Properties

Molecular Weight:  74.08
Volume:  82.438
LogP:  -1.372
LogD:  -2.075
LogS:  1.111
# Rotatable Bonds:  2
TPSA:  52.04
# H-Bond Aceptor:  2
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.455
Synthetic Accessibility Score:  2.323
Fsp3:  1.0
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:  -6.249
MDCK Permeability:  0.000832940568216145
Pgp-inhibitor:  0.009
Pgp-substrate:  0.015
Human Intestinal Absorption (HIA):  0.041
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.34
Plasma Protein Binding (PPB):  9.856592178344727%
Volume Distribution (VD):  1.187
Pgp-substrate:  90.33316040039062%

ADMET: Metabolism

CYP1A2-inhibitor:  0.026
CYP1A2-substrate:  0.097
CYP2C19-inhibitor:  0.019
CYP2C19-substrate:  0.189
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.177
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.893
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.178

ADMET: Excretion

Clearance (CL):  4.965
Half-life (T1/2):  0.524

ADMET: Toxicity

hERG Blockers:  0.037
Human Hepatotoxicity (H-HT):  0.141
Drug-inuced Liver Injury (DILI):  0.029
AMES Toxicity:  0.084
Rat Oral Acute Toxicity:  0.635
Maximum Recommended Daily Dose:  0.118
Skin Sensitization:  0.857
Carcinogencity:  0.129
Eye Corrosion:  0.998
Eye Irritation:  0.106
Respiratory Toxicity:  0.749

Download Data

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

  Natural Product: NPC309715

Natural Product ID:  NPC309715
Common Name*:   Propane-1,3-Diamine
IUPAC Name:   propane-1,3-diamine
Synonyms:   Propane-1,3-Diamine
Standard InCHIKey:  XFNJVJPLKCPIBV-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C3H10N2/c4-2-1-3-5/h1-5H2
SMILES:  NCCCN
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL174324
PubChem CID:   428
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0002449] Amines
          • [CHEMONTID:0002450] Primary amines
            • [CHEMONTID:0000469] Monoalkylamines

*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
NPT1886 Cell Line J774 Mus musculus Activity = 100.0 % PMID[503745]
NPT1886 Cell Line J774 Mus musculus Activity = 94.0 % PMID[503745]
NPT1886 Cell Line J774 Mus musculus Activity = 89.0 % PMID[503745]
NPT27 Others Unspecified Activity = 5.0 % PMID[503744]
NPT35 Others n.a. CLogP = -1.49 n.a. PMID[503744]
NPT1496 Protein Complex Glutamate NMDA receptor Rattus norvegicus Sp Max = 22.0 % PMID[503744]
NPT1496 Protein Complex Glutamate NMDA receptor Rattus norvegicus Sp St = 98.0 % PMID[503744]
NPT35 Others n.a. pK1 = 10.55 n.a. PMID[503744]
NPT35 Others n.a. pK2 = 8.69 n.a. PMID[503744]
NPT35 Others n.a. LogP = 1.86 n.a. PMID[503744]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 20000.0 nM PMID[503747]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 19952.62 nM PMID[503747]

☑ 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 NPC309715 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
0.85 High Similarity NPC309330
0.85 High Similarity NPC28081
0.7727 Intermediate Similarity NPC306277
0.7727 Intermediate Similarity NPC318947
0.7619 Intermediate Similarity NPC27869
0.72 Intermediate Similarity NPC27675
0.6923 Remote Similarity NPC193536
0.6667 Remote Similarity NPC125872
0.6667 Remote Similarity NPC83032
0.6429 Remote Similarity NPC95589
0.6296 Remote Similarity NPC152949
0.625 Remote Similarity NPC119368
0.6207 Remote Similarity NPC320889
0.5926 Remote Similarity NPC8576
0.5833 Remote Similarity NPC326253
0.5714 Remote Similarity NPC270175
0.5714 Remote Similarity NPC232311
0.5714 Remote Similarity NPC313882

  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 NPC309715 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
0.85 High Similarity NPD8560 Clinical (unspecified phase)
0.8421 Intermediate Similarity NPD7383 Phase 3
0.6957 Remote Similarity NPD8221 Clinical (unspecified phase)
0.6429 Remote Similarity NPD401 Approved
0.6207 Remote Similarity NPD1156 Clinical (unspecified phase)
0.6154 Remote Similarity NPD8791 Clinical (unspecified phase)
0.6 Remote Similarity NPD2276 Clinical (unspecified phase)
0.5926 Remote Similarity NPD9063 Approved
0.5926 Remote Similarity NPD9013 Clinical (unspecified phase)
0.5926 Remote Similarity NPD9064 Approved
0.5926 Remote Similarity NPD9012 Phase 2
0.5862 Remote Similarity NPD9040 Clinical (unspecified phase)
0.5862 Remote Similarity NPD9039 Approved
0.5862 Remote Similarity NPD9041 Approved
0.5833 Remote Similarity NPD7382 Approved
0.5833 Remote Similarity NPD7381 Approved
0.5714 Remote Similarity NPD9465 Approved
0.5714 Remote Similarity NPD8544 Approved
0.5667 Remote Similarity NPD8948 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