Structure

Physi-Chem Properties

Molecular Weight:  175.01
Volume:  161.228
LogP:  1.062
LogD:  -0.016
LogS:  -1.072
# Rotatable Bonds:  4
TPSA:  35.42
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.28
Synthetic Accessibility Score:  5.704
Fsp3:  0.5
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:  -4.455
MDCK Permeability:  3.9876373193692416e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.03
Human Intestinal Absorption (HIA):  0.046
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.031

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.478
Plasma Protein Binding (PPB):  35.10023498535156%
Volume Distribution (VD):  0.875
Pgp-substrate:  77.83125305175781%

ADMET: Metabolism

CYP1A2-inhibitor:  0.019
CYP1A2-substrate:  0.347
CYP2C19-inhibitor:  0.019
CYP2C19-substrate:  0.591
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.433
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.596
CYP3A4-inhibitor:  0.012
CYP3A4-substrate:  0.107

ADMET: Excretion

Clearance (CL):  5.766
Half-life (T1/2):  0.863

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.255
Drug-inuced Liver Injury (DILI):  0.267
AMES Toxicity:  0.381
Rat Oral Acute Toxicity:  0.954
Maximum Recommended Daily Dose:  0.912
Skin Sensitization:  0.763
Carcinogencity:  0.768
Eye Corrosion:  0.821
Eye Irritation:  0.898
Respiratory Toxicity:  0.977

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

  Natural Product: NPC205586

Natural Product ID:  NPC205586
Common Name*:   (E)-4-Isothiocyanato-1-Methylsulfinylbut-1-Ene
IUPAC Name:   (E)-4-isothiocyanato-1-methylsulfinylbut-1-ene
Synonyms:  
Standard InCHIKey:  QKGJFQMGPDVOQE-HWKANZROSA-N
Standard InCHI:  InChI=1S/C6H9NOS2/c1-10(8)5-3-2-4-7-6-9/h3,5H,2,4H2,1H3/b5-3+
SMILES:  CS(=O)/C=C/CCN=C=S
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL49659
PubChem CID:   6433206
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0000491] Sulfoxides

*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
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota heartwood n.a. n.a. PMID[23743282]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[24176362]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota seeds n.a. n.a. PMID[25466198]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[9525107]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17706 Caragana tibetica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17408 Derris amazonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15441 Lotus pedunculatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17408 Derris amazonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17706 Caragana tibetica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15441 Lotus pedunculatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15441 Lotus pedunculatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18117 Dalbergia odorifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17706 Caragana tibetica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7539 Raphanus sativus Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17408 Derris amazonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15441 Lotus pedunculatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18117 Dalbergia odorifera 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
NPT440 Individual Protein Quinone oxidoreductase Mus musculus CD = 0.4 uM PMID[522474]
NPT1083 Cell Line A-375 Homo sapiens Inhibition = 84.1 % PMID[522475]
NPT1083 Cell Line A-375 Homo sapiens Inhibition = 50.24 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Inhibition = 79.22 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Inhibition = 89.32 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens IC50 = 6410.0 nM PMID[522475]
NPT81 Cell Line A549 Homo sapiens IC50 = 9330.0 nM PMID[522475]
NPT1083 Cell Line A-375 Homo sapiens IC50 = 18740.0 nM PMID[522475]
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 31920.0 nM PMID[522475]
NPT165 Cell Line HeLa Homo sapiens IC50 = 85050.0 nM PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Activity = 5.94 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Activity = 5.79 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Activity = 8.37 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Activity = 79.91 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Activity = 9.77 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Activity = 12.24 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Activity = 22.85 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Activity = 55.14 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Activity = 75.66 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Activity = 6.42 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Activity = 17.92 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Activity = 65.76 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Activity = 8.56 % PMID[522475]
NPT659 Cell Line SMMC-7721 Homo sapiens Activity = 25.68 % PMID[522475]
NPT35 Others n.a. Drug degradation = 60.0 % PMID[522475]

☑ 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 NPC205586 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
0.7222 Intermediate Similarity NPC27723
0.7105 Intermediate Similarity NPC138865
0.7 Intermediate Similarity NPC292366
0.7 Intermediate Similarity NPC171713
0.7 Intermediate Similarity NPC105023
0.6667 Remote Similarity NPC140734
0.6667 Remote Similarity NPC180872
0.6579 Remote Similarity NPC172064
0.6486 Remote Similarity NPC46648
0.6486 Remote Similarity NPC144939
0.6364 Remote Similarity NPC149602
0.6222 Remote Similarity NPC145077
0.6216 Remote Similarity NPC2088
0.6 Remote Similarity NPC168614
0.6 Remote Similarity NPC204251
0.5833 Remote Similarity NPC142438
0.5814 Remote Similarity NPC266113
0.58 Remote Similarity NPC282097
0.5763 Remote Similarity NPC324077

  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 NPC205586 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
0.6486 Remote Similarity NPD8580 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