Structure

Physi-Chem Properties

Molecular Weight:  156.01
Volume:  150.181
LogP:  3.226
LogD:  3.526
LogS:  -4.205
# Rotatable Bonds:  2
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.604
Synthetic Accessibility Score:  2.309
Fsp3:  0.143
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.168
MDCK Permeability:  2.1862544599571265e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.109
30% Bioavailability (F30%):  0.653

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.913
Plasma Protein Binding (PPB):  69.76895141601562%
Volume Distribution (VD):  3.565
Pgp-substrate:  24.039094924926758%

ADMET: Metabolism

CYP1A2-inhibitor:  0.985
CYP1A2-substrate:  0.871
CYP2C19-inhibitor:  0.954
CYP2C19-substrate:  0.678
CYP2C9-inhibitor:  0.846
CYP2C9-substrate:  0.542
CYP2D6-inhibitor:  0.027
CYP2D6-substrate:  0.337
CYP3A4-inhibitor:  0.018
CYP3A4-substrate:  0.44

ADMET: Excretion

Clearance (CL):  13.287
Half-life (T1/2):  0.32

ADMET: Toxicity

hERG Blockers:  0.195
Human Hepatotoxicity (H-HT):  0.079
Drug-inuced Liver Injury (DILI):  0.722
AMES Toxicity:  0.674
Rat Oral Acute Toxicity:  0.285
Maximum Recommended Daily Dose:  0.032
Skin Sensitization:  0.946
Carcinogencity:  0.432
Eye Corrosion:  0.975
Eye Irritation:  0.996
Respiratory Toxicity:  0.983

Download Data

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

  Natural Product: NPC469807

Natural Product ID:  NPC469807
Common Name*:   2-(Methyldithio)Benzene
IUPAC Name:   (methyldisulfanyl)benzene
Synonyms:   NSC-677545
Standard InCHIKey:  LMSQHVXHZCNJEP-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H8S2/c1-8-9-7-5-3-2-4-6-7/h2-6H,1H3
SMILES:  CSSc1ccccc1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL118504
PubChem CID:   84234
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives

*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
NPO13010 Allium stipitatum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[19093848]
NPO13010 Allium stipitatum Species Amaryllidaceae Eukaryota n.a. bulb n.a. PMID[19093848]
NPO13010 Allium stipitatum Species Amaryllidaceae 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
NPT24 Organism Human immunodeficiency virus 1 Human immunodeficiency virus 1 IC50 = 7.9 n.a. PMID[456107]
NPT1176 Organism Mycobacterium fortuitum Mycobacterium fortuitum MIC > 128.0 ug.mL-1 PMID[456108]
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis MIC = 64.0 ug.mL-1 PMID[456108]
NPT1177 Organism Mycobacterium phlei Mycobacterium phlei MIC > 128.0 ug.mL-1 PMID[456108]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 128.0 ug.mL-1 PMID[456108]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 128.0 ug.mL-1 PMID[456108]

☑ 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 NPC469807 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
0.7963 Intermediate Similarity NPC11150
0.7937 Intermediate Similarity NPC22627
0.7619 Intermediate Similarity NPC45255
0.7424 Intermediate Similarity NPC36440
0.7377 Intermediate Similarity NPC277704
0.7286 Intermediate Similarity NPC212463
0.7258 Intermediate Similarity NPC269586
0.7143 Intermediate Similarity NPC65873
0.7143 Intermediate Similarity NPC212114
0.7143 Intermediate Similarity NPC300345
0.7143 Intermediate Similarity NPC120441
0.7097 Intermediate Similarity NPC149436
0.7031 Intermediate Similarity NPC8235
0.6986 Remote Similarity NPC302129
0.6986 Remote Similarity NPC35599
0.6984 Remote Similarity NPC198841
0.6923 Remote Similarity NPC169110
0.6923 Remote Similarity NPC147062
0.6857 Remote Similarity NPC5324
0.6825 Remote Similarity NPC56072
0.6818 Remote Similarity NPC238023
0.6818 Remote Similarity NPC310758
0.6818 Remote Similarity NPC210849
0.6818 Remote Similarity NPC150196
0.6818 Remote Similarity NPC248705
0.6818 Remote Similarity NPC54368
0.6818 Remote Similarity NPC135924
0.6812 Remote Similarity NPC52330
0.68 Remote Similarity NPC67863
0.6769 Remote Similarity NPC64270
0.6769 Remote Similarity NPC114327
0.6769 Remote Similarity NPC36357
0.6761 Remote Similarity NPC105991
0.6716 Remote Similarity NPC29680
0.6714 Remote Similarity NPC181786
0.6618 Remote Similarity NPC88566
0.6567 Remote Similarity NPC246588
0.6522 Remote Similarity NPC32312
0.6522 Remote Similarity NPC155172
0.6522 Remote Similarity NPC198023
0.6515 Remote Similarity NPC18259
0.6515 Remote Similarity NPC119076
0.6494 Remote Similarity NPC8981
0.6471 Remote Similarity NPC71009
0.6471 Remote Similarity NPC66517
0.6471 Remote Similarity NPC200745
0.6471 Remote Similarity NPC22786
0.6429 Remote Similarity NPC178527
0.6418 Remote Similarity NPC147578
0.641 Remote Similarity NPC195713
0.6377 Remote Similarity NPC113670
0.6377 Remote Similarity NPC21211
0.6377 Remote Similarity NPC45756
0.6338 Remote Similarity NPC267443
0.6338 Remote Similarity NPC6107
0.6324 Remote Similarity NPC200624
0.6324 Remote Similarity NPC134584
0.6286 Remote Similarity NPC291066
0.625 Remote Similarity NPC311343
0.6197 Remote Similarity NPC289915
0.6197 Remote Similarity NPC113837
0.6173 Remote Similarity NPC125549
0.6164 Remote Similarity NPC139416
0.6164 Remote Similarity NPC246822
0.6164 Remote Similarity NPC213570
0.6164 Remote Similarity NPC98880
0.6143 Remote Similarity NPC50266
0.6133 Remote Similarity NPC244738
0.6081 Remote Similarity NPC95289
0.6027 Remote Similarity NPC78954
0.6027 Remote Similarity NPC82770
0.6027 Remote Similarity NPC239931
0.6 Remote Similarity NPC39799
0.6 Remote Similarity NPC326200
0.6 Remote Similarity NPC475573
0.6 Remote Similarity NPC158028
0.6 Remote Similarity NPC226999
0.6 Remote Similarity NPC475289
0.6 Remote Similarity NPC280135
0.6 Remote Similarity NPC193578
0.6 Remote Similarity NPC1008
0.6 Remote Similarity NPC87099
0.6 Remote Similarity NPC74458
0.6 Remote Similarity NPC135433
0.6 Remote Similarity NPC470796
0.5952 Remote Similarity NPC148231
0.5949 Remote Similarity NPC299367
0.5946 Remote Similarity NPC235059
0.5946 Remote Similarity NPC473206
0.5946 Remote Similarity NPC16190
0.5946 Remote Similarity NPC200936
0.5946 Remote Similarity NPC169222
0.5921 Remote Similarity NPC285679
0.5921 Remote Similarity NPC54269
0.5867 Remote Similarity NPC263385
0.5867 Remote Similarity NPC229235
0.5867 Remote Similarity NPC470795
0.5867 Remote Similarity NPC219246
0.5867 Remote Similarity NPC251490
0.5867 Remote Similarity NPC72670
0.5844 Remote Similarity NPC122327
0.5844 Remote Similarity NPC112609
0.5844 Remote Similarity NPC299134
0.5844 Remote Similarity NPC66775
0.5844 Remote Similarity NPC113000
0.5833 Remote Similarity NPC264470
0.5811 Remote Similarity NPC22760
0.5789 Remote Similarity NPC155429
0.5789 Remote Similarity NPC208302
0.5783 Remote Similarity NPC307163
0.5783 Remote Similarity NPC474088
0.5769 Remote Similarity NPC98976
0.5769 Remote Similarity NPC276699
0.5769 Remote Similarity NPC189371
0.5769 Remote Similarity NPC307195
0.5747 Remote Similarity NPC315403
0.5733 Remote Similarity NPC297358
0.5714 Remote Similarity NPC1901
0.5714 Remote Similarity NPC271437
0.5698 Remote Similarity NPC53492
0.5698 Remote Similarity NPC43655
0.5696 Remote Similarity NPC139658
0.5696 Remote Similarity NPC110264
0.5696 Remote Similarity NPC271642
0.5696 Remote Similarity NPC175393
0.5658 Remote Similarity NPC271732
0.5641 Remote Similarity NPC108218
0.5641 Remote Similarity NPC96835
0.5641 Remote Similarity NPC208075
0.5641 Remote Similarity NPC258492
0.5625 Remote Similarity NPC329318
0.5625 Remote Similarity NPC98269
0.5625 Remote Similarity NPC249018
0.5625 Remote Similarity NPC3190
0.5625 Remote Similarity NPC290638
0.5625 Remote Similarity NPC3672
0.5625 Remote Similarity NPC287790
0.5625 Remote Similarity NPC298023
0.5625 Remote Similarity NPC325662

  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 NPC469807 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
0.6833 Remote Similarity NPD9072 Clinical (unspecified phase)
0.6377 Remote Similarity NPD675 Discontinued
0.6375 Remote Similarity NPD9303 Approved
0.6286 Remote Similarity NPD173 Clinical (unspecified phase)
0.625 Remote Similarity NPD9302 Approved
0.6235 Remote Similarity NPD4728 Approved
0.6133 Remote Similarity NPD9728 Phase 1
0.6047 Remote Similarity NPD2811 Clinical (unspecified phase)
0.6 Remote Similarity NPD294 Approved
0.6 Remote Similarity NPD292 Approved
0.5977 Remote Similarity NPD1007 Discontinued
0.5976 Remote Similarity NPD423 Phase 3
0.5946 Remote Similarity NPD9497 Clinical (unspecified phase)
0.5844 Remote Similarity NPD80 Approved
0.5844 Remote Similarity NPD9591 Approved
0.5844 Remote Similarity NPD9594 Approved
0.5844 Remote Similarity NPD9588 Approved
0.5844 Remote Similarity NPD9589 Approved
0.5844 Remote Similarity NPD9592 Approved
0.5844 Remote Similarity NPD9590 Approved
0.5844 Remote Similarity NPD9593 Approved
0.5814 Remote Similarity NPD9184 Approved
0.5814 Remote Similarity NPD9186 Approved
0.5765 Remote Similarity NPD1697 Approved
0.5747 Remote Similarity NPD9108 Approved
0.5733 Remote Similarity NPD1673 Approved
0.5714 Remote Similarity NPD3832 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3456 Approved
0.5714 Remote Similarity NPD3458 Approved
0.5714 Remote Similarity NPD3457 Approved
0.5667 Remote Similarity NPD837 Approved
0.5652 Remote Similarity NPD1672 Phase 2
0.5641 Remote Similarity NPD505 Clinical (unspecified phase)
0.5625 Remote Similarity NPD4147 Approved
0.5625 Remote Similarity NPD603 Approved
0.5625 Remote Similarity NPD4144 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