Structure

Physi-Chem Properties

Molecular Weight:  337.16
Volume:  322.854
LogP:  3.858
LogD:  3.824
LogS:  -4.165
# Rotatable Bonds:  5
TPSA:  96.21
# H-Bond Aceptor:  7
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.372
Synthetic Accessibility Score:  3.26
Fsp3:  0.733
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:  -4.816
MDCK Permeability:  1.737693128234241e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.995
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.797
Plasma Protein Binding (PPB):  95.47005462646484%
Volume Distribution (VD):  1.477
Pgp-substrate:  2.5249979496002197%

ADMET: Metabolism

CYP1A2-inhibitor:  0.746
CYP1A2-substrate:  0.723
CYP2C19-inhibitor:  0.939
CYP2C19-substrate:  0.066
CYP2C9-inhibitor:  0.787
CYP2C9-substrate:  0.409
CYP2D6-inhibitor:  0.91
CYP2D6-substrate:  0.739
CYP3A4-inhibitor:  0.289
CYP3A4-substrate:  0.14

ADMET: Excretion

Clearance (CL):  3.429
Half-life (T1/2):  0.225

ADMET: Toxicity

hERG Blockers:  0.179
Human Hepatotoxicity (H-HT):  0.712
Drug-inuced Liver Injury (DILI):  0.893
AMES Toxicity:  0.91
Rat Oral Acute Toxicity:  0.667
Maximum Recommended Daily Dose:  0.817
Skin Sensitization:  0.484
Carcinogencity:  0.751
Eye Corrosion:  0.004
Eye Irritation:  0.111
Respiratory Toxicity:  0.956

Download Data

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

  Natural Product: NPC293799

Natural Product ID:  NPC293799
Common Name*:   Gs-39783
IUPAC Name:   4-N,6-N-dicyclopentyl-2-methylsulfanyl-5-nitropyrimidine-4,6-diamine
Synonyms:   GS-39783
Standard InCHIKey:  GSGVDKOCBKBMGG-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C15H23N5O2S/c1-23-15-18-13(16-10-6-2-3-7-10)12(20(21)22)14(19-15)17-11-8-4-5-9-11/h10-11H,2-9H2,1H3,(H2,16,17,18,19)
SMILES:  CSc1nc(c(c(=NC2CCCC2)[nH]1)N(=O)=O)NC1CCCC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL392394
PubChem CID:   6604928
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0001202] Thioethers
        • [CHEMONTID:0004631] Aryl thioethers

*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
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. root n.a. PMID[18975262]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. PMID[21465337]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. PMID[24333010]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18176 Ephedra sinica Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18176 Ephedra sinica Species Ephedraceae 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
NPT50 Individual Protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency = 891.3 nM PMID[509856]
NPT213 Individual Protein Cytochrome P450 2C19 Homo sapiens Potency = 5011.9 nM PMID[509856]
NPT150 Individual Protein Anthrax lethal factor Bacillus anthracis Potency = 10000.0 nM PMID[509856]
NPT212 Individual Protein Cytochrome P450 2C9 Homo sapiens Potency = 1995.3 nM PMID[509856]
NPT212 Individual Protein Cytochrome P450 2C9 Homo sapiens AC50 = 1995.26 nM PMID[509856]
NPT213 Individual Protein Cytochrome P450 2C19 Homo sapiens AC50 = 5011.87 nM PMID[509856]
NPT208 Individual Protein Cytochrome P450 1A2 Homo sapiens AC50 = 3981.07 nM PMID[509856]
NPT444 Individual Protein Ubiquitin carboxyl-terminal hydrolase 1 Homo sapiens Potency n.a. 15848.9 nM PMID[509856]
NPT886 Cell Line NIH3T3 Mus musculus IC50 = 60000.0 nM PMID[509857]
NPT1407 Individual Protein GABA-B receptor 1 Homo sapiens %max = 90.4 % PMID[509859]
NPT1407 Individual Protein GABA-B receptor 1 Homo sapiens EC50 = 79.43 nM PMID[509859]
NPT1407 Individual Protein GABA-B receptor 1 Homo sapiens Activity = 0.0 % PMID[509859]
NPT997 Protein Complex GABA-B receptor Homo sapiens Efficacy = 132.0 % PMID[509855]
NPT997 Protein Complex GABA-B receptor Homo sapiens Efficacy = 153.0 % PMID[509855]
NPT997 Protein Complex GABA-B receptor Homo sapiens EC50 = 741.31 nM PMID[509855]
NPT997 Protein Complex GABA-B receptor Homo sapiens Emax = 146.0 % PMID[509855]
NPT197 Protein-Protein Interaction Menin/Histone-lysine N-methyltransferase MLL Homo sapiens Potency = 39810.7 nM PMID[509856]
NPT2 Others Unspecified Potency = 11220.2 nM PMID[509856]
NPT32 Organism Mus musculus Mus musculus TIME = 0.03833 hr PMID[509857]
NPT32 Organism Mus musculus Mus musculus TIME = 0.0 hr PMID[509857]
NPT32 Organism Mus musculus Mus musculus TIME = 0.955 hr PMID[509857]
NPT32 Organism Mus musculus Mus musculus TIME = 1.0 hr PMID[509857]
NPT2 Others Unspecified Activity = 59.0 % PMID[509857]
NPT997 Protein Complex GABA-B receptor Homo sapiens Activity = 192.0 % PMID[509858]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 25.87 % PMID[509860]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = -1.12 % PMID[509861]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 21.48 % PMID[509862]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = -0.1 % PMID[509863]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 0.02 % PMID[509864]

☑ 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 NPC293799 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
NPC

  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 NPC293799 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
0.5904 Remote Similarity NPD9643 Approved
0.5862 Remote Similarity NPD1144 Phase 2
0.5789 Remote Similarity NPD9654 Phase 2

  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