Structure

Physi-Chem Properties

Molecular Weight:  90.03
Volume:  81.015
LogP:  -0.462
LogD:  -0.455
LogS:  -1.348
# Rotatable Bonds:  1
TPSA:  49.87
# H-Bond Aceptor:  2
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.331
Synthetic Accessibility Score:  3.222
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.751
MDCK Permeability:  0.0020638322457671165
Pgp-inhibitor:  0.0
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.072
20% Bioavailability (F20%):  0.023
30% Bioavailability (F30%):  0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.317
Plasma Protein Binding (PPB):  14.1004638671875%
Volume Distribution (VD):  1.056
Pgp-substrate:  88.07605743408203%

ADMET: Metabolism

CYP1A2-inhibitor:  0.051
CYP1A2-substrate:  0.561
CYP2C19-inhibitor:  0.023
CYP2C19-substrate:  0.342
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.087
CYP2D6-inhibitor:  0.029
CYP2D6-substrate:  0.763
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.195

ADMET: Excretion

Clearance (CL):  4.997
Half-life (T1/2):  0.656

ADMET: Toxicity

hERG Blockers:  0.026
Human Hepatotoxicity (H-HT):  0.156
Drug-inuced Liver Injury (DILI):  0.049
AMES Toxicity:  0.037
Rat Oral Acute Toxicity:  0.431
Maximum Recommended Daily Dose:  0.019
Skin Sensitization:  0.306
Carcinogencity:  0.731
Eye Corrosion:  0.325
Eye Irritation:  0.95
Respiratory Toxicity:  0.195

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

  Natural Product: NPC479249

Natural Product ID:  NPC479249
Common Name*:   NNBBQNFHCVVQHZ-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NNBBQNFHCVVQHZ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C2H6N2S.H2O4S/c1-5-2(3)4;1-5(2,3)4/h1H3,(H3,3,4);(H2,1,2,3,4)
SMILES:  CSC(=N)N.OS(=O)(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   75270
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0001232] Isothioureas

*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
NPO10031 Euphorbia antiquorum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[11858748]
NPO12595 Euphorbia royleana Species Euphorbiaceae Eukaryota aerial parts Yuanjiang, Yunnan Province, China 2008-APR PMID[19438253]
NPO10031 Euphorbia antiquorum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[24840014]
NPO14207 Euphorbia neriifolia Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[25252924]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[27933899]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[28960981]
NPO12595 Euphorbia royleana Species Euphorbiaceae Eukaryota Stems n.a. n.a. PMID[30730729]
NPO10031 Euphorbia antiquorum Species Euphorbiaceae Eukaryota Stems n.a. n.a. PMID[31180680]
NPO40777 Ajuga pantantha Species n.a. n.a. n.a. n.a. n.a. PMID[32216313]
NPO14207 Euphorbia neriifolia Species Euphorbiaceae Eukaryota Stems n.a. n.a. PMID[32822173]
NPO12595 Euphorbia royleana Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10031 Euphorbia antiquorum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12595 Euphorbia royleana Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10031 Euphorbia antiquorum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12595 Euphorbia royleana Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12595 Euphorbia royleana Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14207 Euphorbia neriifolia Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10031 Euphorbia antiquorum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17346 Salvia plebeia Species Lamiaceae 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
NPT34 Cell Line BV-2 Mus musculus IC50 = 13200.0 nM PMID[22560584]
NPT270 Individual Protein Nitric oxide synthase, inducible Mus musculus IC50 = 1800.0 nM PMID[27570243]
NPT34 Cell Line BV-2 Mus musculus IC50 = 2900.0 nM PMID[27933899]
NPT34 Cell Line BV-2 Mus musculus IC50 = 2500.0 nM PMID[28377060]
NPT34 Cell Line BV-2 Mus musculus IC50 = 2900.0 nM PMID[27989668]
NPT34 Cell Line BV-2 Mus musculus IC50 = 3700.0 nM PMID[30730729]
NPT34 Cell Line BV-2 Mus musculus IC50 = 3100.0 nM PMID[31180680]
NPT34 Cell Line BV-2 Mus musculus IC50 = 2400.0 nM PMID[32216313]
NPT2 Others Unspecified IC50 = 2000.0 nM PMID[32822173]

☑ 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 NPC479249 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 NPC479249 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