Structure

Physi-Chem Properties

Molecular Weight:  244.16
Volume:  256.645
LogP:  1.459
LogD:  1.585
LogS:  -1.205
# Rotatable Bonds:  0
TPSA:  25.24
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.695
Synthetic Accessibility Score:  4.147
Fsp3:  0.667
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:  -4.681
MDCK Permeability:  1.6596151908743195e-05
Pgp-inhibitor:  0.733
Pgp-substrate:  0.022
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.101
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.973
Plasma Protein Binding (PPB):  26.404525756835938%
Volume Distribution (VD):  4.298
Pgp-substrate:  69.53942108154297%

ADMET: Metabolism

CYP1A2-inhibitor:  0.048
CYP1A2-substrate:  0.554
CYP2C19-inhibitor:  0.053
CYP2C19-substrate:  0.819
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.07
CYP2D6-inhibitor:  0.931
CYP2D6-substrate:  0.865
CYP3A4-inhibitor:  0.021
CYP3A4-substrate:  0.602

ADMET: Excretion

Clearance (CL):  6.372
Half-life (T1/2):  0.374

ADMET: Toxicity

hERG Blockers:  0.339
Human Hepatotoxicity (H-HT):  0.858
Drug-inuced Liver Injury (DILI):  0.413
AMES Toxicity:  0.261
Rat Oral Acute Toxicity:  0.154
Maximum Recommended Daily Dose:  0.903
Skin Sensitization:  0.452
Carcinogencity:  0.814
Eye Corrosion:  0.004
Eye Irritation:  0.118
Respiratory Toxicity:  0.838

Download Data

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

  Natural Product: NPC135639

Natural Product ID:  NPC135639
Common Name*:   FQEQMASDZFXSJI-YNEHKIRRSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FQEQMASDZFXSJI-YNEHKIRRSA-N
Standard InCHI:  InChI=1S/C15H20N2O/c18-15-6-3-5-14-11-8-12(10-17(14)15)13-4-1-2-7-16(13)9-11/h3,5-6,11-13H,1-2,4,7-10H2/t11-,12+,13+/m0/s1
SMILES:  C1CCN2C[C@@H]3C[C@H](Cn4c3cccc4=O)[C@H]2C1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2373362
PubChem CID:   442938
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002719] Lupin alkaloids
        • [CHEMONTID:0002723] Anagyrine-type 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]
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]
NPO19231 Sophora flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
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
NPT48 Individual Protein Lysine-specific demethylase 4D-like Homo sapiens Potency = 25118.9 nM PMID[482664]
NPT963 Organism Hepatitis B virus Hepatitis B virus Activity = 19.8 % PMID[482663]
NPT963 Organism Hepatitis B virus Hepatitis B virus Activity = 0.0 % PMID[482663]
NPT963 Organism Hepatitis B virus Hepatitis B virus Activity = 33.1 % PMID[482663]
NPT197 Protein-Protein Interaction Menin/Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 39810.7 nM PMID[482664]
NPT94 Individual Protein Aldehyde dehydrogenase 1A1 Homo sapiens Potency = 39810.7 nM PMID[482664]
NPT2 Others Unspecified Potency = 0.9 nM PMID[482664]

☑ 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 NPC135639 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
1.0 High Similarity NPC234822
1.0 High Similarity NPC143344
1.0 High Similarity NPC61321
1.0 High Similarity NPC78058
0.9359 High Similarity NPC120699
0.9359 High Similarity NPC127430
0.8861 High Similarity NPC308050
0.8846 High Similarity NPC63284
0.8795 High Similarity NPC207048
0.8734 High Similarity NPC320667
0.8734 High Similarity NPC214125
0.8395 Intermediate Similarity NPC86452
0.8395 Intermediate Similarity NPC244256
0.8193 Intermediate Similarity NPC268580
0.8193 Intermediate Similarity NPC77890
0.8193 Intermediate Similarity NPC267203
0.8193 Intermediate Similarity NPC132858
0.8111 Intermediate Similarity NPC145707
0.7684 Intermediate Similarity NPC91036
0.7449 Intermediate Similarity NPC144714
0.7449 Intermediate Similarity NPC100810
0.7303 Intermediate Similarity NPC255430
0.7157 Intermediate Similarity NPC472856
0.6914 Remote Similarity NPC206660
0.6774 Remote Similarity NPC116881
0.6774 Remote Similarity NPC57163
0.675 Remote Similarity NPC42477
0.6667 Remote Similarity NPC477461
0.6667 Remote Similarity NPC477459
0.6556 Remote Similarity NPC25513
0.6514 Remote Similarity NPC143173
0.6506 Remote Similarity NPC476559
0.6322 Remote Similarity NPC48448
0.6322 Remote Similarity NPC290231
0.6322 Remote Similarity NPC206241
0.6322 Remote Similarity NPC68043
0.6322 Remote Similarity NPC180401
0.6322 Remote Similarity NPC271803
0.6322 Remote Similarity NPC266383
0.6296 Remote Similarity NPC231129
0.6289 Remote Similarity NPC157479
0.6279 Remote Similarity NPC76869
0.6279 Remote Similarity NPC477460
0.6265 Remote Similarity NPC252684
0.622 Remote Similarity NPC82919
0.6186 Remote Similarity NPC147513
0.6154 Remote Similarity NPC34672
0.6129 Remote Similarity NPC28529
0.6098 Remote Similarity NPC385
0.6061 Remote Similarity NPC305602
0.6061 Remote Similarity NPC17497
0.6042 Remote Similarity NPC215474
0.604 Remote Similarity NPC473056
0.6024 Remote Similarity NPC133923
0.602 Remote Similarity NPC76283
0.6 Remote Similarity NPC476560
0.5978 Remote Similarity NPC80447
0.5957 Remote Similarity NPC473446
0.5957 Remote Similarity NPC473695
0.5833 Remote Similarity NPC474001
0.5833 Remote Similarity NPC209232
0.5773 Remote Similarity NPC90150
0.5769 Remote Similarity NPC247316
0.575 Remote Similarity NPC228980
0.575 Remote Similarity NPC243635
0.575 Remote Similarity NPC151004
0.5701 Remote Similarity NPC472258
0.566 Remote Similarity NPC256452
0.5638 Remote Similarity NPC281154

  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 NPC135639 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
0.8193 Intermediate Similarity NPD529 Approved
0.6744 Remote Similarity NPD816 Approved
0.6744 Remote Similarity NPD815 Approved
0.6422 Remote Similarity NPD4063 Clinical (unspecified phase)
0.5902 Remote Similarity NPD3549 Approved
0.5902 Remote Similarity NPD3550 Clinical (unspecified phase)
0.5902 Remote Similarity NPD3547 Approved
0.575 Remote Similarity NPD1821 Approved
0.575 Remote Similarity NPD1823 Approved
0.575 Remote Similarity NPD1822 Approved
0.5641 Remote Similarity NPD5180 Approved
0.5641 Remote Similarity NPD5179 Approved
0.5641 Remote Similarity NPD5181 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