Structure

Physi-Chem Properties

Molecular Weight:  113.03
Volume:  116.633
LogP:  2.605
LogD:  1.709
LogS:  -1.541
# Rotatable Bonds:  2
TPSA:  12.36
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.394
Synthetic Accessibility Score:  4.316
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.409
MDCK Permeability:  3.0419656468438916e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.117
Plasma Protein Binding (PPB):  16.3585147857666%
Volume Distribution (VD):  1.052
Pgp-substrate:  79.24571990966797%

ADMET: Metabolism

CYP1A2-inhibitor:  0.596
CYP1A2-substrate:  0.554
CYP2C19-inhibitor:  0.028
CYP2C19-substrate:  0.854
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.813
CYP2D6-inhibitor:  0.016
CYP2D6-substrate:  0.874
CYP3A4-inhibitor:  0.028
CYP3A4-substrate:  0.262

ADMET: Excretion

Clearance (CL):  7.187
Half-life (T1/2):  0.725

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.571
Drug-inuced Liver Injury (DILI):  0.495
AMES Toxicity:  0.517
Rat Oral Acute Toxicity:  0.789
Maximum Recommended Daily Dose:  0.098
Skin Sensitization:  0.652
Carcinogencity:  0.748
Eye Corrosion:  0.925
Eye Irritation:  0.991
Respiratory Toxicity:  0.966

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

  Natural Product: NPC163528

Natural Product ID:  NPC163528
Common Name*:   XDDPFUCCKIMFOG-ONEGZZNKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XDDPFUCCKIMFOG-ONEGZZNKSA-N
Standard InCHI:  InChI=1S/C5H7NS/c1-2-3-4-6-5-7/h3-4H,2H2,1H3/b4-3+
SMILES:  CC/C=C/N=C=S
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   6439701
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0001234] Isothiocyanates

*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
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2004.07.004]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[11551759]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[17011103]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. whole plant n.a. PMID[21214467]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[25700090]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota Roots n.a. Database[FooDB]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3634 Robinia pseudoacacia 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
NPT449 Organism Meloidogyne javanica Meloidogyne javanica mortality = 49.92 % PMID[528103]
NPT449 Organism Meloidogyne javanica Meloidogyne javanica mortality = 20.56 % PMID[528103]

☑ 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 NPC163528 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 NPC163528 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