Structure

Physi-Chem Properties

Molecular Weight:  299.13
Volume:  260.076
LogP:  -2.129
LogD:  -0.648
LogS:  -1.344
# Rotatable Bonds:  3
TPSA:  184.81
# H-Bond Aceptor:  11
# H-Bond Donor:  9
# Rings:  3
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.28
Synthetic Accessibility Score:  5.275
Fsp3:  0.7
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.103
MDCK Permeability:  0.0001435819867765531
Pgp-inhibitor:  0.001
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.855
20% Bioavailability (F20%):  0.98
30% Bioavailability (F30%):  0.354

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.2
Plasma Protein Binding (PPB):  14.536650657653809%
Volume Distribution (VD):  0.626
Pgp-substrate:  71.15155792236328%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.043
CYP2C19-inhibitor:  0.014
CYP2C19-substrate:  0.06
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.044
CYP2D6-inhibitor:  0.086
CYP2D6-substrate:  0.199
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.05

ADMET: Excretion

Clearance (CL):  2.427
Half-life (T1/2):  0.367

ADMET: Toxicity

hERG Blockers:  0.22
Human Hepatotoxicity (H-HT):  0.175
Drug-inuced Liver Injury (DILI):  0.272
AMES Toxicity:  0.804
Rat Oral Acute Toxicity:  0.937
Maximum Recommended Daily Dose:  0.898
Skin Sensitization:  0.307
Carcinogencity:  0.994
Eye Corrosion:  0.003
Eye Irritation:  0.007
Respiratory Toxicity:  0.955

Download Data

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

  Natural Product: NPC305648

Natural Product ID:  NPC305648
Common Name*:   RPQXVSUAYFXFJA-HGRQIUPRSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RPQXVSUAYFXFJA-HGRQIUPRSA-N
Standard InCHI:  InChI=1S/C10H17N7O4/c11-6-15-5-4(3-21-8(13)18)14-7(12)17-2-1-9(19,20)10(5,17)16-6/h4-5,19-20H,1-3H2,(H2,12,14)(H2,13,18)(H3,11,15,16)/t4-,5-,10-/m0/s1
SMILES:  C1CN2C(=N)N[C@@H](COC(=N)O)[C@H]3[C@]2(C1(O)O)NC(=N)N3
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   56947150
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0001800] Saxitoxins, gonyautoxins, and derivatives

*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
NPO2446 Gentiana verna Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0021-9673(00)89757-5]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota leaves n.a. n.a. PMID[12568545]
NPO25825 Saussurea lappa Species Asteraceae Eukaryota Roots n.a. n.a. PMID[14510592]
NPO30603 Saussurea lappa n.a. n.a. n.a. n.a. root n.a. PMID[18409040]
NPO30603 Saussurea lappa n.a. n.a. n.a. roots n.a. n.a. PMID[18579374]
NPO18534 Alexandrium tamarense Species Pyrocystaceae Eukaryota n.a. n.a. n.a. PMID[18698820]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[19191562]
NPO24241 Taiwania cryptomerioides Species Cupressaceae Eukaryota n.a. twig n.a. PMID[22474975]
NPO30633 Acanthopanax sessiliflorus n.a. n.a. n.a. Fruits n.a. n.a. PMID[22691179]
NPO30603 Saussurea lappa n.a. n.a. n.a. n.a. n.a. n.a. PMID[25068579]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota Whole Plants n.a. n.a. PMID[28093914]
NPO24241 Taiwania cryptomerioides Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[31347365]
NPO25825 Saussurea lappa Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[3572418]
NPO11614 Dianthus chinensis Species Caryophyllaceae Eukaryota n.a. aerial part n.a. PMID[7764590]
NPO30603 Saussurea lappa n.a. n.a. n.a. n.a. root n.a. PMID[8541643]
NPO24241 Taiwania cryptomerioides Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[9014350]
NPO30633 Acanthopanax sessiliflorus n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO22976 Ruta microcarpa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20275 Juniperus sabina Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3451 Saxidomus giganteus Species Veneridae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11614 Dianthus chinensis Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2756 Emerita analoga Species Hippidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30603 Saussurea lappa n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24241 Taiwania cryptomerioides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20275 Juniperus sabina Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22976 Ruta microcarpa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11614 Dianthus chinensis Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11809 Eleutherococcus sessiliflorus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3451 Saxidomus giganteus Species Veneridae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25825 Saussurea lappa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24241 Taiwania cryptomerioides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2756 Emerita analoga Species Hippidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11614 Dianthus chinensis Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20275 Juniperus sabina Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24241 Taiwania cryptomerioides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30633 Acanthopanax sessiliflorus n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22976 Ruta microcarpa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11614 Dianthus chinensis Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25825 Saussurea lappa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11809 Eleutherococcus sessiliflorus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2756 Emerita analoga Species Hippidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11614 Dianthus chinensis Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18534 Alexandrium tamarense Species Pyrocystaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20275 Juniperus sabina Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24241 Taiwania cryptomerioides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3451 Saxidomus giganteus Species Veneridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25825 Saussurea lappa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22976 Ruta microcarpa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2446 Gentiana verna Species Gentianaceae 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
NPT3708 Individual Protein Sodium channel protein type IX alpha subunit Homo sapiens IC50 = 702.0 nM PMID[30139550]
NPT3716 Individual Protein Sodium channel protein type I alpha subunit Homo sapiens IC50 = 2.3 nM PMID[31012583]
NPT3715 Individual Protein Sodium channel protein type II alpha subunit Homo sapiens IC50 = 1.0 nM PMID[31012583]
NPT3714 Individual Protein Sodium channel protein type III alpha subunit Homo sapiens IC50 = 13.0 nM PMID[31012583]
NPT3713 Individual Protein Sodium channel protein type IV alpha subunit Homo sapiens IC50 = 19.0 nM PMID[31012583]
NPT2856 Individual Protein Sodium channel protein type V alpha subunit Homo sapiens IC50 = 210.0 nM PMID[31012583]
NPT3712 Individual Protein Sodium channel protein type VIII alpha subunit Homo sapiens IC50 = 1.1 nM PMID[31012583]
NPT3710 Individual Protein Sodium channel protein type X alpha subunit Homo sapiens IC50 > 10000.0 nM PMID[31012583]
NPT3711 Individual Protein Sodium channel protein type XI alpha subunit Homo sapiens IC50 > 10000.0 nM PMID[31012583]
NPT2 Others Unspecified Ratio IC50 < 1.0 n.a. PMID[31012583]
NPT2 Others Unspecified Ratio IC50 > 20.0 n.a. PMID[31012583]
NPT27660 SINGLE PROTEIN Sodium channel protein type VII alpha subunit Homo sapiens IC50 = 410.0 nM PMID[31012583]

☑ 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 NPC305648 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 NPC305648 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