Structure

Physi-Chem Properties

Molecular Weight:  248.19
Volume:  261.918
LogP:  1.723
LogD:  1.123
LogS:  -1.776
# Rotatable Bonds:  0
TPSA:  23.55
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.653
Synthetic Accessibility Score:  3.707
Fsp3:  0.933
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.757
MDCK Permeability:  9.583254723111168e-06
Pgp-inhibitor:  0.129
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.021
20% Bioavailability (F20%):  0.182
30% Bioavailability (F30%):  0.064

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.923
Plasma Protein Binding (PPB):  14.94756031036377%
Volume Distribution (VD):  1.698
Pgp-substrate:  72.26567840576172%

ADMET: Metabolism

CYP1A2-inhibitor:  0.029
CYP1A2-substrate:  0.119
CYP2C19-inhibitor:  0.041
CYP2C19-substrate:  0.88
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.066
CYP2D6-inhibitor:  0.664
CYP2D6-substrate:  0.769
CYP3A4-inhibitor:  0.023
CYP3A4-substrate:  0.635

ADMET: Excretion

Clearance (CL):  12.592
Half-life (T1/2):  0.346

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.61
Drug-inuced Liver Injury (DILI):  0.055
AMES Toxicity:  0.021
Rat Oral Acute Toxicity:  0.546
Maximum Recommended Daily Dose:  0.79
Skin Sensitization:  0.183
Carcinogencity:  0.379
Eye Corrosion:  0.003
Eye Irritation:  0.024
Respiratory Toxicity:  0.313

Download Data

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

  Natural Product: NPC206241

Natural Product ID:  NPC206241
Common Name*:   ZSBXGIUJOOQZMP-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZSBXGIUJOOQZMP-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C15H24N2O/c18-14-7-1-6-13-12-5-3-9-16-8-2-4-11(15(12)16)10-17(13)14/h11-13,15H,1-10H2
SMILES:  C1CC2C3CCCN4CCCC(CN2C(=O)C1)C34
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1733145
PubChem CID:   285698
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002719] Lupin alkaloids
        • [CHEMONTID:0002720] Matrine alkaloids

*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
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[10654410]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. root n.a. PMID[10843587]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota Roots n.a. n.a. PMID[15568770]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. root n.a. PMID[16392664]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota roots Hualien Hsien, Taiwan 2003-JUL PMID[16933887]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. root n.a. PMID[16933887]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. root n.a. PMID[17951038]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18175961]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24295087]
NPO7715 Sophora tonkinensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24345512]
NPO7715 Sophora tonkinensis Species Fabaceae Eukaryota root n.a. n.a. PMID[24959987]
NPO20471 Sophora alopecuroides Species Fabaceae Eukaryota root bark Mongolian n.a. PMID[26073007]
NPO7715 Sophora tonkinensis Species Fabaceae Eukaryota Rhizomes Nanning, Guangxi Province, China 2012-Dec PMID[26132528]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[27575476]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota Roots n.a. n.a. PMID[30298740]
NPO7715 Sophora tonkinensis Species Fabaceae Eukaryota Roots; Rhizomes n.a. n.a. PMID[30698432]
NPO20471 Sophora alopecuroides Species Fabaceae Eukaryota Aerial Parts n.a. n.a. PMID[31747283]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota Roots n.a. n.a. PMID[9868163]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. root n.a. Database[Article]
NPO20471 Sophora alopecuroides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24584 Corydalis bungeana Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16483 Herba sophorae alopecuroidis n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20471 Sophora alopecuroides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24584 Corydalis bungeana Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20471 Sophora alopecuroides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7715 Sophora tonkinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24584 Corydalis bungeana Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7715 Sophora tonkinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7715 Sophora tonkinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20471 Sophora alopecuroides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24584 Corydalis bungeana Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19231 Sophora flavescens Species Fabaceae 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
NPT443 Individual Protein Histone acetyltransferase GCN5 Homo sapiens Potency n.a. 31622.8 nM PMID[466140]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 131.2 nM PMID[466140]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 92.8 nM PMID[466140]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Potency n.a. 26.6 nM PMID[466141]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Potency n.a. 6.7 nM PMID[466141]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Potency n.a. 14950.2 nM PMID[466141]

☑ 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 NPC206241 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
1.0 High Similarity NPC68043
1.0 High Similarity NPC271803
1.0 High Similarity NPC180401
1.0 High Similarity NPC48448
1.0 High Similarity NPC266383
1.0 High Similarity NPC290231
0.9275 High Similarity NPC80447
0.8312 Intermediate Similarity NPC124359
0.7901 Intermediate Similarity NPC168017
0.7711 Intermediate Similarity NPC178632
0.7564 Intermediate Similarity NPC268580
0.75 Intermediate Similarity NPC151004
0.75 Intermediate Similarity NPC228980
0.75 Intermediate Similarity NPC243635
0.7089 Intermediate Similarity NPC308050
0.6867 Remote Similarity NPC255430
0.6707 Remote Similarity NPC127430
0.6707 Remote Similarity NPC120699
0.6324 Remote Similarity NPC248956
0.6322 Remote Similarity NPC61321
0.6322 Remote Similarity NPC78058
0.6322 Remote Similarity NPC207048
0.6322 Remote Similarity NPC135639
0.6322 Remote Similarity NPC234822
0.6322 Remote Similarity NPC143344
0.6222 Remote Similarity NPC237535
0.6136 Remote Similarity NPC57163
0.6136 Remote Similarity NPC116881
0.6 Remote Similarity NPC39308
0.5926 Remote Similarity NPC255050
0.5926 Remote Similarity NPC127553
0.5851 Remote Similarity NPC145707
0.5732 Remote Similarity NPC473442
0.5732 Remote Similarity NPC120167
0.5714 Remote Similarity NPC17770
0.5714 Remote Similarity NPC34811
0.5692 Remote Similarity NPC141914

  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 NPC206241 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
0.75 Intermediate Similarity NPD1821 Approved
0.75 Intermediate Similarity NPD1822 Approved
0.75 Intermediate Similarity NPD1823 Approved
0.6707 Remote Similarity NPD7155 Clinical (unspecified phase)
0.6364 Remote Similarity NPD3176 Clinical (unspecified phase)
0.6087 Remote Similarity NPD6934 Discontinued
0.6056 Remote Similarity NPD3727 Discontinued
0.5862 Remote Similarity NPD3155 Clinical (unspecified phase)
0.5811 Remote Similarity NPD605 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