Structure

Physi-Chem Properties

Molecular Weight:  204.13
Volume:  213.313
LogP:  0.87
LogD:  0.963
LogS:  -0.098
# Rotatable Bonds:  0
TPSA:  34.03
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.678
Synthetic Accessibility Score:  4.584
Fsp3:  0.583
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:  -4.851
MDCK Permeability:  3.247634367653518e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.034
30% Bioavailability (F30%):  0.19

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.933
Plasma Protein Binding (PPB):  13.883352279663086%
Volume Distribution (VD):  2.234
Pgp-substrate:  74.08631134033203%

ADMET: Metabolism

CYP1A2-inhibitor:  0.077
CYP1A2-substrate:  0.126
CYP2C19-inhibitor:  0.035
CYP2C19-substrate:  0.844
CYP2C9-inhibitor:  0.009
CYP2C9-substrate:  0.116
CYP2D6-inhibitor:  0.357
CYP2D6-substrate:  0.487
CYP3A4-inhibitor:  0.312
CYP3A4-substrate:  0.444

ADMET: Excretion

Clearance (CL):  8.484
Half-life (T1/2):  0.257

ADMET: Toxicity

hERG Blockers:  0.085
Human Hepatotoxicity (H-HT):  0.433
Drug-inuced Liver Injury (DILI):  0.065
AMES Toxicity:  0.358
Rat Oral Acute Toxicity:  0.903
Maximum Recommended Daily Dose:  0.914
Skin Sensitization:  0.119
Carcinogencity:  0.314
Eye Corrosion:  0.004
Eye Irritation:  0.019
Respiratory Toxicity:  0.809

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General Info & Identifiers & Properties  
Structure MOL file  
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Similar NPs/Drugs  

  Natural Product: NPC57020

Natural Product ID:  NPC57020
Common Name*:   RGKIXECTVPHJLM-AGROOBSYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RGKIXECTVPHJLM-AGROOBSYSA-N
Standard InCHI:  InChI=1S/C12H16N2O/c1-8-9-5-13-6-10(8)11-3-2-4-12(15)14(11)7-9/h2-4,8-10,13H,5-7H2,1H3/t8?,9-,10-/m0/s1
SMILES:  CC1[C@H]2CNC[C@@H]1c1cccc(=O)n1C2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002719] Lupin alkaloids
        • [CHEMONTID:0002722] Cytisine and derivatives

*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
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. DOI[10.3923/pjbs.2013.1138.1144]
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]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[16748484]
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]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. leaf n.a. PMID[17262437]
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]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[18326559]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[20597533]
NPO791 Laburnum anagyroides Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[23022271]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Essential oil n.a. n.a. PMID[23163425]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[23656415]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[23865201]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24295087]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. bulb n.a. PMID[24508058]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[25650289]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[25650289]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota garlic skin n.a. n.a. PMID[25726329]
NPO20471 Sophora alopecuroides Species Fabaceae Eukaryota root bark Mongolian n.a. PMID[26073007]
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]
NPO20471 Sophora alopecuroides Species Fabaceae Eukaryota Aerial Parts n.a. n.a. PMID[31747283]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[8350088]
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]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Bulb n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Bulb n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Fruit Juice n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO791 Laburnum anagyroides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29767 Cytisus laburnum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20471 Sophora alopecuroides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5995 Spartium junceum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO5995 Spartium junceum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO791 Laburnum anagyroides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota 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]
NPO5995 Spartium junceum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20471 Sophora alopecuroides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23230 Allium cepa Species Amaryllidaceae 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]
NPO29767 Cytisus laburnum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO791 Laburnum anagyroides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23230 Allium cepa Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5995 Spartium junceum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO791 Laburnum anagyroides 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]

☑ 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

☑ 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 NPC57020 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 NPC57020 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