Structure

Physi-Chem Properties

Molecular Weight:  159.17
Volume:  179.915
LogP:  -0.519
LogD:  -1.859
LogS:  0.887
# 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:  2.085
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:  -6.243
MDCK Permeability:  6.803049018344609e-06
Pgp-inhibitor:  0.306
Pgp-substrate:  0.974
Human Intestinal Absorption (HIA):  0.136
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.032

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.189
Plasma Protein Binding (PPB):  20.442302703857422%
Volume Distribution (VD):  0.923
Pgp-substrate:  92.18418884277344%

ADMET: Metabolism

CYP1A2-inhibitor:  0.013
CYP1A2-substrate:  0.059
CYP2C19-inhibitor:  0.016
CYP2C19-substrate:  0.224
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.05
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.898
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.229

ADMET: Excretion

Clearance (CL):  6.555
Half-life (T1/2):  0.281

ADMET: Toxicity

hERG Blockers:  0.06
Human Hepatotoxicity (H-HT):  0.126
Drug-inuced Liver Injury (DILI):  0.033
AMES Toxicity:  0.032
Rat Oral Acute Toxicity:  0.447
Maximum Recommended Daily Dose:  0.162
Skin Sensitization:  0.945
Carcinogencity:  0.022
Eye Corrosion:  0.996
Eye Irritation:  0.072
Respiratory Toxicity:  0.788

Download Data

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

  Natural Product: NPC320889

Natural Product ID:  NPC320889
Common Name*:   N'-(3-Aminopropyl)Pentane-1,5-Diamine
IUPAC Name:   N'-(3-aminopropyl)pentane-1,5-diamine
Synonyms:  
Standard InCHIKey:  QZBYOYPROVGOGE-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H21N3/c9-5-2-1-3-7-11-8-4-6-10/h11H,1-10H2
SMILES:  NCCCCCNCCCN
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL89035
PubChem CID:   65523
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
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[10.1016/0006-291X(79)91731-5]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. DOI[10.1093/emboj/18.8.2021]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1091286]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[10977898]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1100617]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[11745165]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[11750815]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12369847]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12467448]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[12805358]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. ChEBI[131529]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[13610867]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[13831814]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[14973046]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15031653]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15292242]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[15610037]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[1644759]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[16630633]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[170247]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[17765195]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[179975]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19026742]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19514719]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[19561621]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[21437340]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[21988831]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22289691]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[22855027]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23537328]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[23676670]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[241475]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24206068]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24783849]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24831709]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24939187]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24966042]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[24967680]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[2543976]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[25867074]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26195826]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26337258]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26670289]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[26826371]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[29897754]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[30302998]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[318639]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[3283102]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[398096]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4877125]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4879561]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[4908789]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[5332408]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6102982]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6284709]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[6338507]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[7042909]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[7601837]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[8852895]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[9470222]
NPO730 Escherichia coli Species Enterobacteriaceae Bacteria 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
NPT2 Others Unspecified Ki = 8030.0 nM PMID[510141]

☑ 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 NPC320889 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
0.9 High Similarity NPC95589
0.8966 High Similarity NPC152949
0.8966 High Similarity NPC193536
0.8788 High Similarity NPC74599
0.8621 High Similarity NPC27675
0.8333 Intermediate Similarity NPC270175
0.8286 Intermediate Similarity NPC326791
0.7812 Intermediate Similarity NPC21157
0.7297 Intermediate Similarity NPC473035
0.7241 Intermediate Similarity NPC306277
0.7188 Intermediate Similarity NPC232311
0.7105 Intermediate Similarity NPC240230
0.7105 Intermediate Similarity NPC167301
0.6923 Remote Similarity NPC321202
0.6842 Remote Similarity NPC270319
0.6757 Remote Similarity NPC203203
0.675 Remote Similarity NPC319114
0.675 Remote Similarity NPC15231
0.6667 Remote Similarity NPC313882
0.6667 Remote Similarity NPC119368
0.6552 Remote Similarity NPC28081
0.6552 Remote Similarity NPC309330
0.6452 Remote Similarity NPC125872
0.6207 Remote Similarity NPC309715
0.6053 Remote Similarity NPC163099
0.6 Remote Similarity NPC27869
0.5882 Remote Similarity NPC8576
0.5625 Remote Similarity NPC110136

  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 NPC320889 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
0.9 High Similarity NPD401 Approved
0.8286 Intermediate Similarity NPD2707 Clinical (unspecified phase)
0.8125 Intermediate Similarity NPD1156 Clinical (unspecified phase)
0.7879 Intermediate Similarity NPD2276 Clinical (unspecified phase)
0.7188 Intermediate Similarity NPD9465 Approved
0.6923 Remote Similarity NPD2273 Clinical (unspecified phase)
0.6875 Remote Similarity NPD9063 Approved
0.6875 Remote Similarity NPD9064 Approved
0.675 Remote Similarity NPD9227 Discontinued
0.6585 Remote Similarity NPD9458 Approved
0.6552 Remote Similarity NPD8560 Clinical (unspecified phase)
0.65 Remote Similarity NPD1463 Clinical (unspecified phase)
0.619 Remote Similarity NPD390 Approved
0.619 Remote Similarity NPD718 Approved
0.6176 Remote Similarity NPD8544 Approved
0.6111 Remote Similarity NPD2275 Approved
0.6111 Remote Similarity NPD5384 Approved
0.6111 Remote Similarity NPD5385 Approved
0.6111 Remote Similarity NPD2274 Approved
0.6087 Remote Similarity NPD395 Approved
0.6087 Remote Similarity NPD396 Approved
0.6061 Remote Similarity NPD8791 Clinical (unspecified phase)
0.6053 Remote Similarity NPD1832 Approved
0.6053 Remote Similarity NPD1833 Approved
0.5882 Remote Similarity NPD9013 Clinical (unspecified phase)
0.5882 Remote Similarity NPD9012 Phase 2
0.5833 Remote Similarity NPD9040 Clinical (unspecified phase)
0.5833 Remote Similarity NPD2705 Approved
0.5833 Remote Similarity NPD2706 Approved
0.5833 Remote Similarity NPD9041 Approved
0.5833 Remote Similarity NPD3734 Approved
0.5833 Remote Similarity NPD9039 Approved
0.5778 Remote Similarity NPD1154 Phase 3
0.575 Remote Similarity NPD9059 Approved
0.5714 Remote Similarity NPD8822 Approved
0.5676 Remote Similarity NPD8948 Approved
0.5652 Remote Similarity NPD9459 Approved
0.5652 Remote Similarity NPD9460 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