Structure

Physi-Chem Properties

Molecular Weight:  203.08
Volume:  206.962
LogP:  4.205
LogD:  2.861
LogS:  -4.276
# Rotatable Bonds:  8
TPSA:  12.36
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.34
Synthetic Accessibility Score:  2.851
Fsp3:  0.889
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.598
MDCK Permeability:  3.260668381699361e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.903
Plasma Protein Binding (PPB):  33.162353515625%
Volume Distribution (VD):  1.381
Pgp-substrate:  54.929630279541016%

ADMET: Metabolism

CYP1A2-inhibitor:  0.577
CYP1A2-substrate:  0.616
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.495
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.086
CYP2D6-inhibitor:  0.062
CYP2D6-substrate:  0.481
CYP3A4-inhibitor:  0.142
CYP3A4-substrate:  0.265

ADMET: Excretion

Clearance (CL):  7.553
Half-life (T1/2):  0.3

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.05
Drug-inuced Liver Injury (DILI):  0.594
AMES Toxicity:  0.167
Rat Oral Acute Toxicity:  0.344
Maximum Recommended Daily Dose:  0.224
Skin Sensitization:  0.93
Carcinogencity:  0.222
Eye Corrosion:  0.947
Eye Irritation:  0.986
Respiratory Toxicity:  0.965

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

  Natural Product: NPC235767

Natural Product ID:  NPC235767
Common Name*:   (7-Isothiocyanatoheptyl)(Methyl)Sulfane
IUPAC Name:   1-isothiocyanato-7-methylsulfanylheptane
Synonyms:  
Standard InCHIKey:  LDIRGNDMTOGVRB-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H17NS2/c1-12-8-6-4-2-3-5-7-10-9-11/h2-8H2,1H3
SMILES:  CSCCCCCCCN=C=S
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3593948
PubChem CID:   10125146
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
NPO28141 Colpomenia sinuosa Species Scytosiphonaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/np50097a033]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. fruit n.a. PMID[12802735]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. fruit n.a. PMID[18384095]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. leaf n.a. PMID[22014120]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. fruit n.a. PMID[22014120]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. leaf n.a. PMID[22014168]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. n.a. n.a. PMID[23540838]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. n.a. n.a. PMID[24295708]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. leaf n.a. PMID[25102361]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. fruit n.a. PMID[25306330]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. n.a. Database[FooDB]
NPO28608 Olea europaea Species Oleaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO28608 Olea europaea Species Oleaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28070 Chrysosplenium americanum Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21557 Woodsia manchuriensis Species Woodsiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20714 Lobophytum schoedei Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28608 Olea europaea Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23326 Bohadschia vitiensis Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28422 Sabia japonica Species Sabiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28646 Streptomyces argenteolus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO28195 Phlogacanthus tubiflorus Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28141 Colpomenia sinuosa Species Scytosiphonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27829 Aplophyllum pedicellatum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO27905 Eritrichium sericeum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28556 Streptomyces pentaticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO28263 Anemone tomentosa Species Ranunculaceae 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
NPT346 Individual Protein Transient receptor potential cation channel subfamily A member 1 Homo sapiens EC50 = 610.0 nM PMID[537323]
NPT346 Individual Protein Transient receptor potential cation channel subfamily A member 1 Homo sapiens max activation = 90.0 % PMID[537323]

☑ 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 NPC235767 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
0.9412 High Similarity NPC266113
0.8421 Intermediate Similarity NPC149602
0.7941 Intermediate Similarity NPC172064
0.7895 Intermediate Similarity NPC140734
0.7368 Intermediate Similarity NPC292366
0.7368 Intermediate Similarity NPC171713
0.7368 Intermediate Similarity NPC105023
0.7 Intermediate Similarity NPC180872
0.6765 Remote Similarity NPC106203
0.6176 Remote Similarity NPC245814

  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 NPC235767 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
NPD

  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