Structure

Physi-Chem Properties

Molecular Weight:  264.18
Volume:  270.708
LogP:  0.179
LogD:  0.796
LogS:  -0.135
# 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:  0.495
Synthetic Accessibility Score:  4.636
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:  -5.554
MDCK Permeability:  1.3397071597864851e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.986
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.158
Plasma Protein Binding (PPB):  10.618270874023438%
Volume Distribution (VD):  0.96
Pgp-substrate:  82.74810028076172%

ADMET: Metabolism

CYP1A2-inhibitor:  0.021
CYP1A2-substrate:  0.291
CYP2C19-inhibitor:  0.042
CYP2C19-substrate:  0.39
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.161
CYP2D6-inhibitor:  0.014
CYP2D6-substrate:  0.225
CYP3A4-inhibitor:  0.032
CYP3A4-substrate:  0.358

ADMET: Excretion

Clearance (CL):  10.769
Half-life (T1/2):  0.945

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.796
Drug-inuced Liver Injury (DILI):  0.11
AMES Toxicity:  0.026
Rat Oral Acute Toxicity:  0.074
Maximum Recommended Daily Dose:  0.902
Skin Sensitization:  0.663
Carcinogencity:  0.81
Eye Corrosion:  0.036
Eye Irritation:  0.077
Respiratory Toxicity:  0.591

Download Data

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

  Natural Product: NPC80447

Natural Product ID:  NPC80447
Common Name*:   Oxymatrine
IUPAC Name:   n.a.
Synonyms:   Oxymatrine
Standard InCHIKey:  XVPBINOPNYFXID-LHDUFFHYSA-N
Standard InCHI:  InChI=1S/C15H24N2O2/c18-14-7-1-6-13-12-5-3-9-17(19)8-2-4-11(15(12)17)10-16(13)14/h11-13,15H,1-10H2/t11-,12+,13+,15-,17?/m0/s1
SMILES:  O=C1CCC[C@H]2N1C[C@@H]1CCCN3(=O)[C@@H]1[C@@H]2CCC3
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL458337
PubChem CID:   114850
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]
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]
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[490171]
NPT135 Individual Protein Chromobox protein homolog 1 Homo sapiens Potency n.a. 100000.0 nM PMID[490176]
NPT11 Individual Protein Guanine nucleotide-binding protein G(s), subunit alpha Homo sapiens Potency n.a. 5011.9 nM PMID[490176]
NPT616 Cell Line MDCK Canis lupus familiaris CC50 > 80000.0 nM PMID[490178]
NPT963 Organism Hepatitis B virus Hepatitis B virus Activity = 39.7 % PMID[490171]
NPT963 Organism Hepatitis B virus Hepatitis B virus Activity = 35.3 % PMID[490171]
NPT963 Organism Hepatitis B virus Hepatitis B virus Activity = 17.1 % PMID[490171]
NPT963 Organism Hepatitis B virus Hepatitis B virus Activity = 15.8 % PMID[490171]
NPT963 Organism Hepatitis B virus Hepatitis B virus EC50 = 31.0 ug.mL-1 PMID[490173]
NPT963 Organism Hepatitis B virus Hepatitis B virus Inhibition = 43.0 % PMID[490173]
NPT963 Organism Hepatitis B virus Hepatitis B virus Activity = 60.0 % PMID[490173]
NPT963 Organism Hepatitis B virus Hepatitis B virus Inhibition = 62.0 % PMID[490173]
NPT24647 CELL-LINE HepG2 2.2.15 Homo sapiens Inhibition = 50.0 % PMID[490173]
NPT610 Others Molecular identity unknown Activity = 50.0 % PMID[490173]
NPT27 Others Unspecified MTT = 3.12 mg/ml PMID[490173]
NPT27 Others Unspecified Ratio CC50/IC50 = 100.0 n.a. PMID[490173]
NPT963 Organism Hepatitis B virus Hepatitis B virus Inhibition = 75.0 % PMID[490173]
NPT963 Organism Hepatitis B virus Hepatitis B virus Activity = 54.0 % PMID[490173]
NPT1308 Tissue Blood Homo sapiens T1/2 = 2.4 hr PMID[490173]
NPT963 Organism Hepatitis B virus Hepatitis B virus log10cfu = 1.5 n.a. PMID[490173]
NPT24647 CELL-LINE HepG2 2.2.15 Homo sapiens Inhibition = 55.0 % PMID[490174]
NPT24647 CELL-LINE HepG2 2.2.15 Homo sapiens Inhibition = 52.0 % PMID[490175]
NPT963 Organism Hepatitis B virus Hepatitis B virus Activity = 56.0 % PMID[490175]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 1852.6 nM PMID[490176]
NPT2 Others Unspecified Potency n.a. 2818.4 nM PMID[490176]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Potency n.a. 21117.7 nM PMID[490177]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Potency n.a. 0.7 nM PMID[490177]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Potency n.a. 10583.9 nM PMID[490177]
NPT1453 Organism Influenza A virus (A/PR/8/34(H1N1)) Influenza A virus (A/Puerto Rico/8/1934(H1N1)) EC50 > 80000.0 nM PMID[490178]
NPT963 Organism Hepatitis B virus Hepatitis B virus Inhibition = 38.3 % PMID[490181]
NPT963 Organism Hepatitis B virus Hepatitis B virus Inhibition = 20.3 % PMID[490181]
NPT24647 CELL-LINE HepG2 2.2.15 Homo sapiens GI >= 25.0 % PMID[490181]

☑ 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 NPC80447 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
0.9275 High Similarity NPC206241
0.9275 High Similarity NPC68043
0.9275 High Similarity NPC180401
0.9275 High Similarity NPC266383
0.9275 High Similarity NPC290231
0.9275 High Similarity NPC271803
0.9275 High Similarity NPC48448
0.8025 Intermediate Similarity NPC124359
0.7647 Intermediate Similarity NPC168017
0.7471 Intermediate Similarity NPC178632
0.7108 Intermediate Similarity NPC268580
0.6957 Remote Similarity NPC243635
0.6957 Remote Similarity NPC151004
0.6957 Remote Similarity NPC228980
0.6897 Remote Similarity NPC207048
0.6667 Remote Similarity NPC308050
0.6477 Remote Similarity NPC255430
0.6322 Remote Similarity NPC120699
0.6322 Remote Similarity NPC127430
0.6064 Remote Similarity NPC237535
0.5978 Remote Similarity NPC143344
0.5978 Remote Similarity NPC78058
0.5978 Remote Similarity NPC234822
0.5978 Remote Similarity NPC61321
0.5978 Remote Similarity NPC135639
0.589 Remote Similarity NPC248956
0.5806 Remote Similarity NPC57163
0.5806 Remote Similarity NPC116881
0.5765 Remote Similarity NPC255050
0.5765 Remote Similarity NPC127553
0.5714 Remote Similarity NPC145707
0.5667 Remote Similarity NPC39308
0.566 Remote Similarity NPC472856

  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 NPC80447 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
0.6957 Remote Similarity NPD1822 Approved
0.6957 Remote Similarity NPD1823 Approved
0.6957 Remote Similarity NPD1821 Approved
0.6322 Remote Similarity NPD7155 Clinical (unspecified phase)
0.6196 Remote Similarity NPD3176 Clinical (unspecified phase)
0.5938 Remote Similarity NPD6934 Discontinued
0.5714 Remote Similarity NPD3155 Clinical (unspecified phase)
0.5658 Remote Similarity NPD3727 Discontinued
0.5641 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