Structure

Physi-Chem Properties

Molecular Weight:  248.19
Volume:  261.918
LogP:  1.303
LogD:  1.711
LogS:  -1.426
# 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:  4.359
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:  -4.875
MDCK Permeability:  9.565257641952485e-06
Pgp-inhibitor:  0.008
Pgp-substrate:  0.992
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.94
30% Bioavailability (F30%):  0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.513
Plasma Protein Binding (PPB):  18.060230255126953%
Volume Distribution (VD):  1.551
Pgp-substrate:  70.4162826538086%

ADMET: Metabolism

CYP1A2-inhibitor:  0.021
CYP1A2-substrate:  0.082
CYP2C19-inhibitor:  0.039
CYP2C19-substrate:  0.783
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.047
CYP2D6-inhibitor:  0.741
CYP2D6-substrate:  0.501
CYP3A4-inhibitor:  0.015
CYP3A4-substrate:  0.728

ADMET: Excretion

Clearance (CL):  6.648
Half-life (T1/2):  0.697

ADMET: Toxicity

hERG Blockers:  0.054
Human Hepatotoxicity (H-HT):  0.965
Drug-inuced Liver Injury (DILI):  0.79
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.033
Maximum Recommended Daily Dose:  0.173
Skin Sensitization:  0.946
Carcinogencity:  0.404
Eye Corrosion:  0.194
Eye Irritation:  0.493
Respiratory Toxicity:  0.904

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

  Natural Product: NPC258244

Natural Product ID:  NPC258244
Common Name*:   JYIJIIVLEOETIQ-SYQHCUMBSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JYIJIIVLEOETIQ-SYQHCUMBSA-N
Standard InCHI:  InChI=1S/C15H24N2O/c18-15-6-3-5-14-11-8-12(10-17(14)15)13-4-1-2-7-16(13)9-11/h11-14H,1-10H2/t11-,12-,13-,14+/m1/s1
SMILES:  C1CCN2C[C@H]3C[C@H](CN4[C@H]3CCCC4=O)[C@H]2C1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   7018997
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002719] Lupin alkaloids
        • [CHEMONTID:0001795] Sparteine, lupanine, and related 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 n.a. root n.a. PMID[16933887]
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[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]
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]
NPO21386 Catenicella cribraria Species Catenicellidae Eukaryota n.a. n.a. n.a. PMID[8277321]
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]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13593 Cladonia chlorophaea Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
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]
NPO14584 Pinus orientalis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28745 Heterotheca villosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21386 Catenicella cribraria Species Catenicellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO269 Leptospermum polygalifolium Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11675 Kyllinga erecta Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13593 Cladonia chlorophaea Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3543 Araliorhamnus vaginata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO10573 Lilium mackliniae Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12723 Pteronia paniculata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28753 Saccopetalum tomentosum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO28566 Calceolaria lepida Species Calceolariaceae 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 NPC258244 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 NPC258244 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