Structure

Physi-Chem Properties

Molecular Weight:  262.17
Volume:  268.071
LogP:  0.057
LogD:  0.736
LogS:  0.29
# Rotatable Bonds:  0
TPSA:  43.37
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.492
Synthetic Accessibility Score:  5.023
Fsp3:  0.8
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:  -5.475
MDCK Permeability:  1.2930169759783894e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.987
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.354
Plasma Protein Binding (PPB):  16.044462203979492%
Volume Distribution (VD):  0.78
Pgp-substrate:  68.52881622314453%

ADMET: Metabolism

CYP1A2-inhibitor:  0.026
CYP1A2-substrate:  0.251
CYP2C19-inhibitor:  0.035
CYP2C19-substrate:  0.558
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.206
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.293
CYP3A4-inhibitor:  0.022
CYP3A4-substrate:  0.251

ADMET: Excretion

Clearance (CL):  7.505
Half-life (T1/2):  0.952

ADMET: Toxicity

hERG Blockers:  0.023
Human Hepatotoxicity (H-HT):  0.688
Drug-inuced Liver Injury (DILI):  0.136
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.774
Maximum Recommended Daily Dose:  0.773
Skin Sensitization:  0.915
Carcinogencity:  0.88
Eye Corrosion:  0.536
Eye Irritation:  0.272
Respiratory Toxicity:  0.949

Download Data

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

  Natural Product: NPC207048

Natural Product ID:  NPC207048
Common Name*:   Oxysophocarpine
IUPAC Name:   n.a.
Synonyms:   Oxysophocarpine
Standard InCHIKey:  QMGGMESMCJCABO-LHDUFFHYSA-N
Standard InCHI:  InChI=1S/C15H22N2O2/c18-14-7-1-6-13-12-5-3-9-17(19)8-2-4-11(15(12)17)10-16(13)14/h1,7,11-13,15H,2-6,8-10H2/t11-,12+,13+,15-,17?/m0/s1
SMILES:  C1=CC(=O)N2C[C@@H]3CCCN4(=O)CCC[C@H]([C@H]2C1)[C@H]34
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL380410
PubChem CID:   161544
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 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]
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]
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]
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]
NPO19231 Sophora flavescens 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[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]
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
NPT65 Cell Line HepG2 Homo sapiens Activity >= 25.0 % PMID[510285]
NPT616 Cell Line MDCK Canis lupus familiaris TC50 > 762.34 uM PMID[510287]
NPT963 Organism Hepatitis B virus Hepatitis B virus Activity = 48.3 % PMID[510285]
NPT963 Organism Hepatitis B virus Hepatitis B virus Activity = 39.9 % PMID[510285]
NPT963 Organism Hepatitis B virus Hepatitis B virus Activity = 24.6 % PMID[510285]
NPT963 Organism Hepatitis B virus Hepatitis B virus Activity = 22.4 % PMID[510285]
NPT24647 CELL-LINE HepG2 2.2.15 Homo sapiens Inhibition = 15.3 % PMID[510286]
NPT742 Organism Influenza A virus Influenza A virus IC50 = 402820.0 nM PMID[510287]
NPT2 Others Unspecified Selectivity Index > 1.9 n.a. PMID[510287]
NPT3041 Organism Human enterovirus 71 Human enterovirus 71 Activity = 25.0 % PMID[510288]
NPT3041 Organism Human enterovirus 71 Human enterovirus 71 Activity = 30.0 % PMID[510288]

☑ 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 NPC207048 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
0.9359 High Similarity NPC120699
0.9359 High Similarity NPC127430
0.8861 High Similarity NPC308050
0.8795 High Similarity NPC78058
0.8795 High Similarity NPC61321
0.8795 High Similarity NPC234822
0.8795 High Similarity NPC135639
0.8795 High Similarity NPC143344
0.8315 Intermediate Similarity NPC145707
0.8041 Intermediate Similarity NPC472856
0.7872 Intermediate Similarity NPC91036
0.7765 Intermediate Similarity NPC268580
0.7711 Intermediate Similarity NPC63284
0.7629 Intermediate Similarity NPC100810
0.7629 Intermediate Similarity NPC144714
0.7619 Intermediate Similarity NPC320667
0.7619 Intermediate Similarity NPC214125
0.7529 Intermediate Similarity NPC86452
0.7529 Intermediate Similarity NPC244256
0.7159 Intermediate Similarity NPC77890
0.7159 Intermediate Similarity NPC267203
0.7159 Intermediate Similarity NPC132858
0.6923 Remote Similarity NPC255430
0.6897 Remote Similarity NPC80447
0.6774 Remote Similarity NPC57163
0.6774 Remote Similarity NPC116881
0.6506 Remote Similarity NPC206660
0.6463 Remote Similarity NPC477461
0.6463 Remote Similarity NPC477459
0.6341 Remote Similarity NPC42477
0.6322 Remote Similarity NPC48448
0.6322 Remote Similarity NPC206241
0.6322 Remote Similarity NPC271803
0.6322 Remote Similarity NPC290231
0.6322 Remote Similarity NPC266383
0.6322 Remote Similarity NPC180401
0.6322 Remote Similarity NPC68043
0.6296 Remote Similarity NPC231129
0.6289 Remote Similarity NPC157479
0.622 Remote Similarity NPC82919
0.6216 Remote Similarity NPC143173
0.6186 Remote Similarity NPC147513
0.6186 Remote Similarity NPC76283
0.6118 Remote Similarity NPC476559
0.6092 Remote Similarity NPC477460
0.6092 Remote Similarity NPC76869
0.6042 Remote Similarity NPC215474
0.5978 Remote Similarity NPC34672
0.5882 Remote Similarity NPC473056
0.5882 Remote Similarity NPC252684
0.5773 Remote Similarity NPC90150
0.575 Remote Similarity NPC228980
0.575 Remote Similarity NPC243635
0.575 Remote Similarity NPC151004
0.5743 Remote Similarity NPC305602
0.5743 Remote Similarity NPC17497
0.5714 Remote Similarity NPC385
0.5684 Remote Similarity NPC25513
0.567 Remote Similarity NPC476560
0.567 Remote Similarity NPC209232
0.566 Remote Similarity NPC119225
0.566 Remote Similarity NPC471635
0.566 Remote Similarity NPC25033
0.566 Remote Similarity NPC476261
0.566 Remote Similarity NPC470382
0.5657 Remote Similarity NPC124359
0.5647 Remote Similarity NPC133923
0.5625 Remote Similarity NPC473446
0.5625 Remote Similarity NPC28529
0.5625 Remote Similarity NPC473695
0.5619 Remote Similarity NPC247316

  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 NPC207048 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
0.7159 Intermediate Similarity NPD529 Approved
0.6364 Remote Similarity NPD816 Approved
0.6364 Remote Similarity NPD815 Approved
0.575 Remote Similarity NPD1821 Approved
0.575 Remote Similarity NPD1823 Approved
0.575 Remote Similarity NPD1822 Approved
0.5702 Remote Similarity NPD4063 Clinical (unspecified phase)
0.5645 Remote Similarity NPD3547 Approved
0.5645 Remote Similarity NPD3550 Clinical (unspecified phase)
0.5645 Remote Similarity NPD3549 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