Structure

Physi-Chem Properties

Molecular Weight:  810.51
Volume:  827.241
LogP:  4.851
LogD:  4.4
LogS:  -4.072
# Rotatable Bonds:  10
TPSA:  204.83
# H-Bond Aceptor:  13
# H-Bond Donor:  7
# Rings:  6
# Heavy Atoms:  13

MedChem Properties

QED Drug-Likeness Score:  0.101
Synthetic Accessibility Score:  6.12
Fsp3:  0.932
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.312
MDCK Permeability:  7.098681817296892e-05
Pgp-inhibitor:  0.998
Pgp-substrate:  0.395
Human Intestinal Absorption (HIA):  0.717
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.929

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  80.35408782958984%
Volume Distribution (VD):  0.744
Pgp-substrate:  9.46322250366211%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.111
CYP2C19-inhibitor:  0.005
CYP2C19-substrate:  0.658
CYP2C9-inhibitor:  0.036
CYP2C9-substrate:  0.049
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.078
CYP3A4-inhibitor:  0.119
CYP3A4-substrate:  0.129

ADMET: Excretion

Clearance (CL):  0.869
Half-life (T1/2):  0.365

ADMET: Toxicity

hERG Blockers:  0.425
Human Hepatotoxicity (H-HT):  0.159
Drug-inuced Liver Injury (DILI):  0.053
AMES Toxicity:  0.058
Rat Oral Acute Toxicity:  0.058
Maximum Recommended Daily Dose:  0.004
Skin Sensitization:  0.601
Carcinogencity:  0.012
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.466

Download Data

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

  Natural Product: NPC51917

Natural Product ID:  NPC51917
Common Name*:   Propyl Isothiocyanate
IUPAC Name:   1-isothiocyanatopropane
Synonyms:  
Standard InCHIKey:  KKASGUHLXWAKEZ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H7NS/c1-2-3-5-4-6/h2-3H2,1H3
SMILES:  CCCN=C=S
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2251726
PubChem CID:   69403
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
NPO28777 Ardisiae japonicae n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO28777 Ardisiae japonicae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]

☑ 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
NPT114 Cell Line LoVo Homo sapiens IC50 = 181000.0 nM PMID[538216]
NPT449 Organism Meloidogyne javanica Meloidogyne javanica mortality = 40.23 % PMID[538214]
NPT449 Organism Meloidogyne javanica Meloidogyne javanica mortality = 21.53 % PMID[538214]
NPT529 Organism Rhizoctonia solani Rhizoctonia solani GI = 93.71 % PMID[538215]
NPT529 Organism Rhizoctonia solani Rhizoctonia solani GI = 21.36 % PMID[538215]
NPT529 Organism Rhizoctonia solani Rhizoctonia solani GI = 84.25 % PMID[538215]
NPT529 Organism Rhizoctonia solani Rhizoctonia solani GI = 67.98 % PMID[538215]
NPT529 Organism Rhizoctonia solani Rhizoctonia solani GI = 50.13 % PMID[538215]
NPT529 Organism Rhizoctonia solani Rhizoctonia solani EC50 = 11.97 ug.mL-1 PMID[538215]
NPT1286 Organism Pectobacterium carotovorum Pectobacterium carotovorum GI = 29.04 % PMID[538215]
NPT1286 Organism Pectobacterium carotovorum Pectobacterium carotovorum GI = 47.04 % PMID[538215]
NPT1286 Organism Pectobacterium carotovorum Pectobacterium carotovorum GI = 76.26 % PMID[538215]
NPT1286 Organism Pectobacterium carotovorum Pectobacterium carotovorum GI = 85.97 % PMID[538215]
NPT1286 Organism Pectobacterium carotovorum Pectobacterium carotovorum GI = 90.65 % PMID[538215]
NPT1286 Organism Pectobacterium carotovorum Pectobacterium carotovorum EC50 = 20.65 ug.mL-1 PMID[538215]
NPT35 Others n.a. LogP = 2.15 n.a. PMID[538215]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 177000.0 nM PMID[538216]

☑ 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 NPC51917 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
0.9048 High Similarity NPC266347
0.9048 High Similarity NPC245814
0.8636 High Similarity NPC133836
0.8261 Intermediate Similarity NPC106203
0.7037 Intermediate Similarity NPC172064
0.6923 Remote Similarity NPC144939
0.6667 Remote Similarity NPC27723
0.6316 Remote Similarity NPC30691
0.6 Remote Similarity NPC138865
0.5938 Remote Similarity NPC292366
0.5938 Remote Similarity NPC266113
0.5938 Remote Similarity NPC171713
0.5938 Remote Similarity NPC105023
0.5833 Remote Similarity NPC329501
0.5714 Remote Similarity NPC322649

  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 NPC51917 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
0.6923 Remote Similarity NPD8580 Approved
0.5909 Remote Similarity NPD8816 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