Structure

Physi-Chem Properties

Molecular Weight:  158.0
Volume:  137.582
LogP:  1.51
LogD:  1.873
LogS:  -2.142
# Rotatable Bonds:  2
TPSA:  25.78
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.484
Synthetic Accessibility Score:  2.924
Fsp3:  0.2
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:  -4.358
MDCK Permeability:  2.9816574169672094e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.026

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.887
Plasma Protein Binding (PPB):  47.42852020263672%
Volume Distribution (VD):  1.063
Pgp-substrate:  42.41011047363281%

ADMET: Metabolism

CYP1A2-inhibitor:  0.688
CYP1A2-substrate:  0.621
CYP2C19-inhibitor:  0.847
CYP2C19-substrate:  0.419
CYP2C9-inhibitor:  0.477
CYP2C9-substrate:  0.504
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.413
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.257

ADMET: Excretion

Clearance (CL):  10.453
Half-life (T1/2):  0.622

ADMET: Toxicity

hERG Blockers:  0.114
Human Hepatotoxicity (H-HT):  0.34
Drug-inuced Liver Injury (DILI):  0.944
AMES Toxicity:  0.83
Rat Oral Acute Toxicity:  0.488
Maximum Recommended Daily Dose:  0.065
Skin Sensitization:  0.968
Carcinogencity:  0.286
Eye Corrosion:  0.979
Eye Irritation:  0.997
Respiratory Toxicity:  0.989

Download Data

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

  Natural Product: NPC476128

Natural Product ID:  NPC476128
Common Name*:   2-(Methyldithio)Pyrimidine
IUPAC Name:   2-(methyldisulfanyl)pyrimidine
Synonyms:   2-(Methyldithio)Pyrimidine
Standard InCHIKey:  NZAUEHNRHSVOMQ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H6N2S2/c1-8-9-5-6-3-2-4-7-5/h2-4H,1H3
SMILES:  CSSC1=NC=CC=N1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL538438
PubChem CID:   12278995
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001346] Diazines
        • [CHEMONTID:0000075] Pyrimidines and pyrimidine 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
NPT1176 Organism Mycobacterium fortuitum Mycobacterium fortuitum MIC = 8.0 ug.mL-1 PMID[515705]
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis MIC = 8.0 ug.mL-1 PMID[515705]
NPT1177 Organism Mycobacterium phlei Mycobacterium phlei MIC = 16.0 ug.mL-1 PMID[515705]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 2.0 ug.mL-1 PMID[515705]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 4.0 ug.mL-1 PMID[515705]

☑ 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 NPC476128 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
0.9213 High Similarity NPC326364
0.8416 Intermediate Similarity NPC222061
0.757 Intermediate Similarity NPC27699
0.7064 Intermediate Similarity NPC163105
0.6789 Remote Similarity NPC75844
0.6667 Remote Similarity NPC329046
0.661 Remote Similarity NPC68938
0.6091 Remote Similarity NPC9639
0.5965 Remote Similarity NPC174114
0.5965 Remote Similarity NPC87981
0.5965 Remote Similarity NPC326248
0.5965 Remote Similarity NPC187191
0.5913 Remote Similarity NPC273327
0.5887 Remote Similarity NPC84268
0.5763 Remote Similarity NPC155498
0.5726 Remote Similarity NPC111132
0.5726 Remote Similarity NPC473901
0.5726 Remote Similarity NPC248627
0.57 Remote Similarity NPC100312
0.5688 Remote Similarity NPC14223
0.568 Remote Similarity NPC189314
0.5678 Remote Similarity NPC18335

  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 NPC476128 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
0.8557 High Similarity NPD9194 Approved
0.8557 High Similarity NPD9193 Approved
0.7732 Intermediate Similarity NPD8565 Clinical (unspecified phase)
0.757 Intermediate Similarity NPD8571 Phase 3
0.6949 Remote Similarity NPD420 Discontinued
0.6833 Remote Similarity NPD1734 Clinical (unspecified phase)
0.6789 Remote Similarity NPD8566 Approved
0.6748 Remote Similarity NPD2191 Discontinued
0.6637 Remote Similarity NPD9071 Phase 3
0.6484 Remote Similarity NPD3678 Phase 2
0.6378 Remote Similarity NPD1705 Discontinued
0.6341 Remote Similarity NPD306 Approved
0.6308 Remote Similarity NPD4763 Clinical (unspecified phase)
0.622 Remote Similarity NPD8832 Approved
0.6212 Remote Similarity NPD2602 Clinical (unspecified phase)
0.6139 Remote Similarity NPD8584 Approved
0.6107 Remote Similarity NPD1264 Phase 2
0.6074 Remote Similarity NPD4765 Approved
0.6074 Remote Similarity NPD4764 Approved
0.6016 Remote Similarity NPD9366 Approved
0.5985 Remote Similarity NPD2618 Phase 1
0.5909 Remote Similarity NPD9210 Phase 2
0.5833 Remote Similarity NPD162 Approved
0.5833 Remote Similarity NPD427 Approved
0.5833 Remote Similarity NPD426 Approved
0.5833 Remote Similarity NPD428 Approved
0.5822 Remote Similarity NPD491 Approved
0.58 Remote Similarity NPD4143 Clinical (unspecified phase)
0.5775 Remote Similarity NPD1988 Phase 1
0.5734 Remote Similarity NPD4709 Approved
0.5726 Remote Similarity NPD8861 Approved
0.5726 Remote Similarity NPD8862 Approved
0.5726 Remote Similarity NPD8859 Approved
0.5714 Remote Similarity NPD174 Discontinued
0.5693 Remote Similarity NPD799 Phase 1
0.568 Remote Similarity NPD8831 Approved
0.568 Remote Similarity NPD8833 Approved
0.5678 Remote Similarity NPD8836 Approved
0.5649 Remote Similarity NPD8826 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