Structure

Physi-Chem Properties

Molecular Weight:  159.17
Volume:  179.915
LogP:  -0.682
LogD:  -2.045
LogS:  0.878
# Rotatable Bonds:  8
TPSA:  64.07
# H-Bond Aceptor:  3
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.439
Synthetic Accessibility Score:  2.063
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:  -6.258
MDCK Permeability:  6.246519205888035e-06
Pgp-inhibitor:  0.447
Pgp-substrate:  0.971
Human Intestinal Absorption (HIA):  0.164
20% Bioavailability (F20%):  0.011
30% Bioavailability (F30%):  0.028

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.181
Plasma Protein Binding (PPB):  21.35559844970703%
Volume Distribution (VD):  0.94
Pgp-substrate:  92.5836181640625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.013
CYP1A2-substrate:  0.058
CYP2C19-inhibitor:  0.016
CYP2C19-substrate:  0.241
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.05
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.899
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.234

ADMET: Excretion

Clearance (CL):  6.521
Half-life (T1/2):  0.285

ADMET: Toxicity

hERG Blockers:  0.061
Human Hepatotoxicity (H-HT):  0.127
Drug-inuced Liver Injury (DILI):  0.033
AMES Toxicity:  0.029
Rat Oral Acute Toxicity:  0.553
Maximum Recommended Daily Dose:  0.159
Skin Sensitization:  0.945
Carcinogencity:  0.022
Eye Corrosion:  0.996
Eye Irritation:  0.073
Respiratory Toxicity:  0.819

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

  Natural Product: NPC152949

Natural Product ID:  NPC152949
Common Name*:   N'-(4-Aminobutyl)Butane-1,4-Diamine
IUPAC Name:   N'-(4-aminobutyl)butane-1,4-diamine
Synonyms:  
Standard InCHIKey:  UODZHRGDSPLRMD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H21N3/c9-5-1-3-7-11-8-4-2-6-10/h11H,1-10H2
SMILES:  C(CCNCCCCN)CN
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL36119
PubChem CID:   368
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
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. PMID[15974602]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17691 Santalum album Species Santalaceae 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 = 556000.0 nM PMID[557080]
NPT396 Cell Line T47D Homo sapiens Ki = 2700.0 nM PMID[557082]
NPT137 Cell Line L1210 Mus musculus IC50 > 100000.0 nM PMID[557083]
NPT137 Cell Line L1210 Mus musculus IC50 = 3000.0 nM PMID[557083]
NPT137 Cell Line L1210 Mus musculus Polyamine = 0.0 % PMID[557083]
NPT137 Cell Line L1210 Mus musculus Polyamine = 4.0 % PMID[557083]
NPT137 Cell Line L1210 Mus musculus Polyamine = 32.0 % PMID[557083]
NPT137 Cell Line L1210 Mus musculus Polyamine = 2.0 % PMID[557083]
NPT137 Cell Line L1210 Mus musculus Polyamine = 21.0 % PMID[557083]
NPT1882 Individual Protein S-adenosylmethionine decarboxylase 1 Mus musculus AdoMetDC = 54.0 % PMID[557083]
NPT2 Others Unspecified Ki = 2300.0 nM PMID[557081]
NPT610 Others Molecular identity unknown Ki = 3400.0 nM PMID[557083]
NPT2 Others Unspecified ODC = 11.0 % PMID[557083]
NPT21877 PROTEIN FAMILY Spermidine/spermine N(1)-acetyltransferase (SAT) Mus musculus SSAT = 430.0 % PMID[557083]

☑ 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 NPC152949 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
0.9286 High Similarity NPC95589
0.9259 High Similarity NPC193536
0.9259 High Similarity NPC270175
0.8966 High Similarity NPC320889
0.8889 High Similarity NPC27675
0.7931 Intermediate Similarity NPC232311
0.7879 Intermediate Similarity NPC74599
0.7429 Intermediate Similarity NPC326791
0.7419 Intermediate Similarity NPC21157
0.7407 Intermediate Similarity NPC119368
0.7308 Intermediate Similarity NPC309330
0.7308 Intermediate Similarity NPC28081
0.7222 Intermediate Similarity NPC240230
0.7027 Intermediate Similarity NPC321202
0.6944 Remote Similarity NPC473035
0.6842 Remote Similarity NPC319114
0.6786 Remote Similarity NPC306277
0.6757 Remote Similarity NPC167301
0.6667 Remote Similarity NPC27869
0.6571 Remote Similarity NPC163099
0.6486 Remote Similarity NPC270319
0.641 Remote Similarity NPC15231
0.6389 Remote Similarity NPC203203
0.6296 Remote Similarity NPC309715
0.625 Remote Similarity NPC313882
0.6071 Remote Similarity NPC258096
0.6 Remote Similarity NPC83032
0.6 Remote Similarity NPC125872
0.5667 Remote Similarity NPC318947

  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 NPC152949 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
0.9286 High Similarity NPD401 Approved
0.8333 Intermediate Similarity NPD1156 Clinical (unspecified phase)
0.8065 Intermediate Similarity NPD2276 Clinical (unspecified phase)
0.7931 Intermediate Similarity NPD9465 Approved
0.7586 Intermediate Similarity NPD9063 Approved
0.7586 Intermediate Similarity NPD9064 Approved
0.7429 Intermediate Similarity NPD2707 Clinical (unspecified phase)
0.7308 Intermediate Similarity NPD8560 Clinical (unspecified phase)
0.7027 Intermediate Similarity NPD2273 Clinical (unspecified phase)
0.6774 Remote Similarity NPD8544 Approved
0.6579 Remote Similarity NPD1463 Clinical (unspecified phase)
0.641 Remote Similarity NPD9227 Discontinued
0.625 Remote Similarity NPD9458 Approved
0.6216 Remote Similarity NPD9059 Approved
0.5926 Remote Similarity NPD7383 Phase 3
0.5854 Remote Similarity NPD718 Approved
0.5854 Remote Similarity NPD390 Approved
0.5814 Remote Similarity NPD1154 Phase 3
0.5778 Remote Similarity NPD396 Approved
0.5778 Remote Similarity NPD395 Approved
0.575 Remote Similarity NPD8822 Approved
0.5714 Remote Similarity NPD5384 Approved
0.5714 Remote Similarity NPD5385 Approved
0.5714 Remote Similarity NPD2274 Approved
0.5714 Remote Similarity NPD2275 Approved
0.5682 Remote Similarity NPD398 Approved
0.5682 Remote Similarity NPD399 Approved
0.5682 Remote Similarity NPD400 Approved
0.5676 Remote Similarity NPD1832 Approved
0.5676 Remote Similarity NPD1833 Approved
0.5625 Remote Similarity NPD8791 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