Structure

Physi-Chem Properties

Molecular Weight:  259.23
Volume:  311.779
LogP:  6.164
LogD:  4.639
LogS:  -6.003
# Rotatable Bonds:  8
TPSA:  12.89
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.54
Synthetic Accessibility Score:  2.365
Fsp3:  0.611
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.758
MDCK Permeability:  1.3623129234474618e-05
Pgp-inhibitor:  0.28
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.675
30% Bioavailability (F30%):  0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.831
Plasma Protein Binding (PPB):  97.89513397216797%
Volume Distribution (VD):  4.28
Pgp-substrate:  2.1170601844787598%

ADMET: Metabolism

CYP1A2-inhibitor:  0.349
CYP1A2-substrate:  0.918
CYP2C19-inhibitor:  0.294
CYP2C19-substrate:  0.85
CYP2C9-inhibitor:  0.191
CYP2C9-substrate:  0.679
CYP2D6-inhibitor:  0.873
CYP2D6-substrate:  0.925
CYP3A4-inhibitor:  0.669
CYP3A4-substrate:  0.196

ADMET: Excretion

Clearance (CL):  4.039
Half-life (T1/2):  0.153

ADMET: Toxicity

hERG Blockers:  0.202
Human Hepatotoxicity (H-HT):  0.34
Drug-inuced Liver Injury (DILI):  0.13
AMES Toxicity:  0.293
Rat Oral Acute Toxicity:  0.168
Maximum Recommended Daily Dose:  0.135
Skin Sensitization:  0.959
Carcinogencity:  0.307
Eye Corrosion:  0.315
Eye Irritation:  0.951
Respiratory Toxicity:  0.908

Download Data

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

  Natural Product: NPC480049

Natural Product ID:  NPC480049
Common Name*:   BQXJCXDOLDLMQE-SEYXRHQNSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BQXJCXDOLDLMQE-SEYXRHQNSA-N
Standard InCHI:  InChI=1S/C18H29N/c1-5-6-7-8-9-10-11-12-13-18-15(2)14-16(3)19-17(18)4/h12-14H,5-11H2,1-4H3/b13-12-
SMILES:  CCCCCCCC/C=Cc1c(C)cc(C)nc1C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   70694935
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000089] Pyridines and derivatives
        • [CHEMONTID:0004152] Methylpyridines

*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
NPO27735 Aniba citrifolia Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[31577436]
NPO27735 Aniba citrifolia Species Lauraceae 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
NPT236 Individual Protein C-C chemokine receptor type 5 Homo sapiens IC50 > 30000.0 nM PMID[22901310]
NPT90 Cell Line DU-145 Homo sapiens ED50 > 30.0 uM PMID[22901310]
NPT306 Cell Line PC-3 Homo sapiens ED50 > 30.0 uM PMID[22901310]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. ED50 > 30.0 uM PMID[22901310]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 > 20000.0 nM PMID[31577436]

☑ 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 NPC480049 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

  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 NPC480049 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

  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