Structure

Physi-Chem Properties

Molecular Weight:  278.16
Volume:  276.862
LogP:  -0.365
LogD:  -0.441
LogS:  -0.415
# Rotatable Bonds:  0
TPSA:  60.44
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.492
Synthetic Accessibility Score:  4.849
Fsp3:  0.867
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:  -5.558
MDCK Permeability:  1.7552769350004382e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.996
Human Intestinal Absorption (HIA):  0.993
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.197
Plasma Protein Binding (PPB):  11.259979248046875%
Volume Distribution (VD):  0.803
Pgp-substrate:  86.52215576171875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.008
CYP1A2-substrate:  0.113
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.189
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.2
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.199
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.272

ADMET: Excretion

Clearance (CL):  10.661
Half-life (T1/2):  0.956

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.358
Drug-inuced Liver Injury (DILI):  0.043
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.222
Maximum Recommended Daily Dose:  0.948
Skin Sensitization:  0.223
Carcinogencity:  0.87
Eye Corrosion:  0.005
Eye Irritation:  0.038
Respiratory Toxicity:  0.161

Download Data

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

  Natural Product: NPC472856

Natural Product ID:  NPC472856
Common Name*:   VHAFSTUPIKPISL-PVKKKEKWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VHAFSTUPIKPISL-PVKKKEKWSA-N
Standard InCHI:  InChI=1S/C15H22N2O3/c18-12-5-6-13(19)16-9-10-3-1-7-17(20)8-2-4-11(14(12)16)15(10)17/h5-6,10-12,14-15,18H,1-4,7-9H2/t10-,11+,12+,14-,15-,17?/m0/s1
SMILES:  C1CC2CN3C(C4C2[N+](C1)(CCC4)[O-])C(C=CC3=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3590536
PubChem CID:   n.a.
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
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]
NPO7715 Sophora tonkinensis Species Fabaceae Eukaryota Roots; Rhizomes n.a. n.a. PMID[30698432]
NPO7715 Sophora tonkinensis 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[TM-MC]
NPO7715 Sophora tonkinensis 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
NPT189 Cell Line Vero Chlorocebus aethiops TC50 = 115.14 uM PMID[467999]
NPT3119 Organism Human coxsackievirus B3 Human coxsackievirus B3 Ratio IC50 = 45.0 n.a. PMID[467999]
NPT3119 Organism Human coxsackievirus B3 Human coxsackievirus B3 IC50 = 26620.0 nM PMID[467999]
NPT2 Others Unspecified Selectivity Index = 4.3 n.a. PMID[467999]

☑ 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 NPC472856 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
0.9588 High Similarity NPC100810
0.9588 High Similarity NPC144714
0.9278 High Similarity NPC91036
0.8571 High Similarity NPC145707
0.8041 Intermediate Similarity NPC207048
0.7526 Intermediate Similarity NPC127430
0.7526 Intermediate Similarity NPC120699
0.7157 Intermediate Similarity NPC78058
0.7157 Intermediate Similarity NPC234822
0.7157 Intermediate Similarity NPC135639
0.7157 Intermediate Similarity NPC143344
0.7157 Intermediate Similarity NPC61321
0.7143 Intermediate Similarity NPC308050
0.6931 Remote Similarity NPC209232
0.6818 Remote Similarity NPC119225
0.6818 Remote Similarity NPC25033
0.6818 Remote Similarity NPC470382
0.6818 Remote Similarity NPC471635
0.6818 Remote Similarity NPC476261
0.6792 Remote Similarity NPC168017
0.6667 Remote Similarity NPC178632
0.6442 Remote Similarity NPC476560
0.6436 Remote Similarity NPC34672
0.641 Remote Similarity NPC473254
0.6408 Remote Similarity NPC473446
0.6408 Remote Similarity NPC473695
0.6356 Remote Similarity NPC477000
0.6356 Remote Similarity NPC477001
0.6355 Remote Similarity NPC475975
0.6348 Remote Similarity NPC270813
0.6346 Remote Similarity NPC268580
0.6337 Remote Similarity NPC470993
0.6337 Remote Similarity NPC470992
0.6311 Remote Similarity NPC244256
0.6311 Remote Similarity NPC86452
0.6293 Remote Similarity NPC316730
0.6275 Remote Similarity NPC63284
0.6262 Remote Similarity NPC124359
0.626 Remote Similarity NPC247902
0.626 Remote Similarity NPC262880
0.6239 Remote Similarity NPC77703
0.6218 Remote Similarity NPC75523
0.6214 Remote Similarity NPC320667
0.6214 Remote Similarity NPC214125
0.6186 Remote Similarity NPC473289
0.6134 Remote Similarity NPC318544
0.6111 Remote Similarity NPC288629
0.6083 Remote Similarity NPC470073
0.5906 Remote Similarity NPC474984
0.5903 Remote Similarity NPC276822
0.5893 Remote Similarity NPC324506
0.5888 Remote Similarity NPC267203
0.5888 Remote Similarity NPC77890
0.5888 Remote Similarity NPC132858
0.5878 Remote Similarity NPC315188
0.5873 Remote Similarity NPC474995
0.5872 Remote Similarity NPC255430
0.5842 Remote Similarity NPC23721
0.5827 Remote Similarity NPC478137
0.582 Remote Similarity NPC133420
0.5806 Remote Similarity NPC476276
0.5806 Remote Similarity NPC207820
0.5785 Remote Similarity NPC247060
0.5785 Remote Similarity NPC50815
0.5781 Remote Similarity NPC272166
0.578 Remote Similarity NPC226982
0.578 Remote Similarity NPC277341
0.5766 Remote Similarity NPC41162
0.5763 Remote Similarity NPC289140
0.576 Remote Similarity NPC274895
0.5748 Remote Similarity NPC469865
0.5741 Remote Similarity NPC90839
0.5739 Remote Similarity NPC17143
0.5739 Remote Similarity NPC47230
0.5714 Remote Similarity NPC475646
0.5691 Remote Similarity NPC475239
0.5682 Remote Similarity NPC477140
0.5682 Remote Similarity NPC477143
0.5682 Remote Similarity NPC13351
0.568 Remote Similarity NPC159367
0.568 Remote Similarity NPC470072
0.566 Remote Similarity NPC80447
0.5656 Remote Similarity NPC471083
0.5649 Remote Similarity NPC470300
0.5649 Remote Similarity NPC474006
0.5645 Remote Similarity NPC55462
0.5645 Remote Similarity NPC476328
0.5625 Remote Similarity NPC116881
0.5625 Remote Similarity NPC314550
0.5625 Remote Similarity NPC57163
0.5614 Remote Similarity NPC473525
0.561 Remote Similarity NPC476877
0.5606 Remote Similarity NPC470788
0.5603 Remote Similarity NPC99864
0.5603 Remote Similarity NPC473056

  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 NPC472856 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
0.5888 Remote Similarity NPD529 Approved
0.5827 Remote Similarity NPD1376 Discontinued
0.5781 Remote Similarity NPD1000 Clinical (unspecified phase)
0.5772 Remote Similarity NPD7333 Discontinued
0.563 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5603 Remote Similarity NPD8415 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