Structure

Physi-Chem Properties

Molecular Weight:  131.14
Volume:  145.323
LogP:  -1.448
LogD:  -2.269
LogS:  0.915
# Rotatable Bonds:  6
TPSA:  64.07
# H-Bond Aceptor:  3
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.417
Synthetic Accessibility Score:  2.203
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:  -6.336
MDCK Permeability:  2.3049289666232653e-05
Pgp-inhibitor:  0.058
Pgp-substrate:  0.974
Human Intestinal Absorption (HIA):  0.07
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.208
Plasma Protein Binding (PPB):  20.57330322265625%
Volume Distribution (VD):  0.912
Pgp-substrate:  89.41624450683594%

ADMET: Metabolism

CYP1A2-inhibitor:  0.008
CYP1A2-substrate:  0.054
CYP2C19-inhibitor:  0.015
CYP2C19-substrate:  0.138
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.052
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.888
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.197

ADMET: Excretion

Clearance (CL):  5.542
Half-life (T1/2):  0.335

ADMET: Toxicity

hERG Blockers:  0.04
Human Hepatotoxicity (H-HT):  0.115
Drug-inuced Liver Injury (DILI):  0.029
AMES Toxicity:  0.072
Rat Oral Acute Toxicity:  0.227
Maximum Recommended Daily Dose:  0.141
Skin Sensitization:  0.935
Carcinogencity:  0.027
Eye Corrosion:  0.995
Eye Irritation:  0.075
Respiratory Toxicity:  0.678

Download Data

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

  Natural Product: NPC27675

Natural Product ID:  NPC27675
Common Name*:   Norspermidine
IUPAC Name:   N'-(3-aminopropyl)propane-1,3-diamine
Synonyms:   Norspermidine
Standard InCHIKey:  OTBHHUPVCYLGQO-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H17N3/c7-3-1-5-9-6-2-4-8/h9H,1-8H2
SMILES:  NCCCNCCCN
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL28743
PubChem CID:   5942
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0002449] Amines
          • [CHEMONTID:0002451] Secondary amines
            • [CHEMONTID:0002228] Dialkylamines

*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
NPO2316 Cyanidium caldarium Species Cyanidiaceae 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
NPT1879 Individual Protein Deoxyhypusine synthase Rattus norvegicus IC50 = 41000.0 nM PMID[546275]
NPT137 Cell Line L1210 Mus musculus T/C = 179.0 % PMID[546277]
NPT396 Cell Line T47D Homo sapiens Ki = 9500.0 nM PMID[546278]
NPT165 Cell Line HeLa Homo sapiens IC50 = 3000000.0 nM PMID[546279]
NPT165 Cell Line HeLa Homo sapiens IC50 = 100000.0 nM PMID[546279]
NPT137 Cell Line L1210 Mus musculus IC50 = 900.0 nM PMID[546280]
NPT137 Cell Line L1210 Mus musculus IC50 = 500.0 nM PMID[546280]
NPT137 Cell Line L1210 Mus musculus Polyamine = 38.0 % PMID[546280]
NPT137 Cell Line L1210 Mus musculus Polyamine = 44.0 % PMID[546280]
NPT137 Cell Line L1210 Mus musculus Polyamine = 113.0 % PMID[546280]
NPT137 Cell Line L1210 Mus musculus Polyamine = 0.0 % PMID[546280]
NPT137 Cell Line L1210 Mus musculus Polyamine = 12.0 % PMID[546280]
NPT137 Cell Line L1210 Mus musculus Polyamine = 83.0 % PMID[546280]
NPT1882 Individual Protein S-adenosylmethionine decarboxylase 1 Mus musculus AdoMetDC = 62.0 % PMID[546280]
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 62596.3 nM PubChem BioAssay data set
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 6206.4 nM PubChem BioAssay data set
NPT106 Individual Protein Peroxisome proliferator-activated receptor delta Homo sapiens Potency n.a. 49722 nM PubChem BioAssay data set
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 55789.1 nM PubChem BioAssay data set
NPT106 Individual Protein Peroxisome proliferator-activated receptor delta Homo sapiens Potency n.a. 62596.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Ki = 5120.0 nM PMID[546276]
NPT1881 Uncleic Acid Calf thymus DNA Bos taurus IC50 = 220000.0 nM PMID[546279]
NPT317 Uncleic Acid Nucleic Acid IC50 = 140000.0 nM PMID[546279]
NPT317 Uncleic Acid Nucleic Acid IC50 = 370000.0 nM PMID[546279]
NPT610 Others Molecular identity unknown Ki = 7200.0 nM PMID[546280]
NPT2 Others Unspecified ODC = 11.0 % PMID[546280]
NPT21877 PROTEIN FAMILY Spermidine/spermine N(1)-acetyltransferase (SAT) Mus musculus SSAT = 150.0 % PMID[546280]
NPT2 Others Unspecified Tm = 77.0 degrees C PMID[546281]
NPT2 Others Unspecified Delta Tm = 12.0 degrees C PMID[546281]
NPT317 Uncleic Acid Nucleic Acid Ka < 0.001 10'6/M PMID[546282]
NPT35 Others n.a. log K = 14.2 n.a. PMID[546283]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa Inhibition = 14.85 % PMID[546285]
NPT747 Organism Acinetobacter baumannii Acinetobacter baumannii Inhibition = 14.39 % PMID[546285]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa Inhibition = -20.69 % PMID[546285]
NPT2 Others Unspecified Percent Effect = -18.95 % PMID[546286]
NPT2 Others Unspecified Percent Effect = -27.73 % PMID[546286]
NPT2 Others Unspecified Percent Effect = 6.533 % PMID[546286]
NPT2 Others Unspecified Potency n.a. 55789.1 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 49722 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 62064.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 62596.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 78134.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 69637.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 55314.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 15723.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 44314.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 6.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 7023.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 8766.8 nM PubChem BioAssay data set

☑ 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 NPC27675 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
0.9615 High Similarity NPC193536
0.8929 High Similarity NPC95589
0.8889 High Similarity NPC152949
0.8621 High Similarity NPC320889
0.8214 Intermediate Similarity NPC270175
0.7692 Intermediate Similarity NPC119368
0.7586 Intermediate Similarity NPC232311
0.7576 Intermediate Similarity NPC74599
0.72 Intermediate Similarity NPC309715
0.7143 Intermediate Similarity NPC326791
0.7097 Intermediate Similarity NPC21157
0.6944 Remote Similarity NPC240230
0.6923 Remote Similarity NPC28081
0.6923 Remote Similarity NPC309330
0.6757 Remote Similarity NPC321202
0.6579 Remote Similarity NPC319114
0.6429 Remote Similarity NPC306277
0.6296 Remote Similarity NPC27869
0.6286 Remote Similarity NPC163099
0.6216 Remote Similarity NPC473035
0.6216 Remote Similarity NPC270319
0.6111 Remote Similarity NPC203203
0.6053 Remote Similarity NPC167301
0.5862 Remote Similarity NPC318947
0.575 Remote Similarity NPC15231
0.5714 Remote Similarity NPC258096
0.5667 Remote Similarity NPC83032
0.5667 Remote Similarity NPC125872

  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 NPC27675 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
0.8929 High Similarity NPD401 Approved
0.8621 High Similarity NPD1156 Clinical (unspecified phase)
0.7857 Intermediate Similarity NPD9064 Approved
0.7857 Intermediate Similarity NPD9063 Approved
0.7742 Intermediate Similarity NPD2276 Clinical (unspecified phase)
0.7586 Intermediate Similarity NPD9465 Approved
0.7143 Intermediate Similarity NPD2707 Clinical (unspecified phase)
0.7 Intermediate Similarity NPD8544 Approved
0.6923 Remote Similarity NPD8560 Clinical (unspecified phase)
0.6757 Remote Similarity NPD1463 Clinical (unspecified phase)
0.6757 Remote Similarity NPD2273 Clinical (unspecified phase)
0.6316 Remote Similarity NPD8822 Approved
0.6154 Remote Similarity NPD7383 Phase 3
0.6154 Remote Similarity NPD9227 Discontinued
0.5952 Remote Similarity NPD1154 Phase 3
0.5946 Remote Similarity NPD9059 Approved
0.561 Remote Similarity NPD9458 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