Structure

Physi-Chem Properties

Molecular Weight:  108.07
Volume:  117.86
LogP:  0.579
LogD:  0.731
LogS:  0.913
# Rotatable Bonds:  0
TPSA:  25.78
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.497
Synthetic Accessibility Score:  2.073
Fsp3:  0.333
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.477
MDCK Permeability:  3.0266804969869554e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.719
Plasma Protein Binding (PPB):  40.2985725402832%
Volume Distribution (VD):  1.702
Pgp-substrate:  68.14584350585938%

ADMET: Metabolism

CYP1A2-inhibitor:  0.301
CYP1A2-substrate:  0.747
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.72
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.441
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.822
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.265

ADMET: Excretion

Clearance (CL):  7.66
Half-life (T1/2):  0.383

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.549
Drug-inuced Liver Injury (DILI):  0.306
AMES Toxicity:  0.025
Rat Oral Acute Toxicity:  0.166
Maximum Recommended Daily Dose:  0.036
Skin Sensitization:  0.832
Carcinogencity:  0.631
Eye Corrosion:  0.938
Eye Irritation:  0.991
Respiratory Toxicity:  0.732

Download Data

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

  Natural Product: NPC204104

Natural Product ID:  NPC204104
Common Name*:   2,5-Dimethylpyrazine
IUPAC Name:   2,5-dimethylpyrazine
Synonyms:   2,5-Dimethyl-Pyrazine
Standard InCHIKey:  LCZUOKDVTBMCMX-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H8N2/c1-5-3-8-6(2)4-7-5/h3-4H,1-2H3
SMILES:  Cc1cnc(C)cn1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL94709
PubChem CID:   31252
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001346] Diazines
        • [CHEMONTID:0000067] Pyrazines

*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

☑ 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
NPO7576 NPC204104 Other Stem 0.038 0.038 0.038 mg/100g Database [DUKE]
NPO15810 NPC204104 Dried Or Powder n.a. 0.001 n.a. n.a. mg/kg DOI[10.1021/jf00055a023]

☑ 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
NPT8 Individual Protein DNA polymerase iota Homo sapiens Potency n.a. 89125.1 nM PMID[505333]

☑ 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 NPC204104 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
0.9855 High Similarity NPC270637
0.971 High Similarity NPC100312
0.8395 Intermediate Similarity NPC277608
0.8375 Intermediate Similarity NPC76536
0.8171 Intermediate Similarity NPC262236
0.7571 Intermediate Similarity NPC229
0.7571 Intermediate Similarity NPC284039
0.7536 Intermediate Similarity NPC158948
0.6633 Remote Similarity NPC317307
0.66 Remote Similarity NPC180417
0.6596 Remote Similarity NPC9639
0.6429 Remote Similarity NPC326248
0.6429 Remote Similarity NPC187191
0.6381 Remote Similarity NPC149621
0.6381 Remote Similarity NPC215597
0.62 Remote Similarity NPC273327
0.6176 Remote Similarity NPC155498
0.6168 Remote Similarity NPC63433
0.6139 Remote Similarity NPC111132
0.5909 Remote Similarity NPC240084
0.5789 Remote Similarity NPC326364
0.5701 Remote Similarity NPC231655
0.5636 Remote Similarity NPC327613
0.5625 Remote Similarity NPC14223
0.5625 Remote Similarity NPC68938

  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 NPC204104 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
0.7571 Intermediate Similarity NPD9394 Clinical (unspecified phase)
0.7558 Intermediate Similarity NPD8835 Approved
0.7222 Intermediate Similarity NPD9101 Discontinued
0.7174 Intermediate Similarity NPD9472 Phase 3
0.6505 Remote Similarity NPD9082 Approved
0.6321 Remote Similarity NPD757 Phase 3
0.6139 Remote Similarity NPD8862 Approved
0.6139 Remote Similarity NPD8861 Approved
0.6139 Remote Similarity NPD8859 Approved
0.5856 Remote Similarity NPD8824 Phase 3
0.5743 Remote Similarity NPD9194 Approved
0.5743 Remote Similarity NPD9193 Approved
0.5701 Remote Similarity NPD9099 Clinical (unspecified phase)
0.5701 Remote Similarity NPD9098 Phase 3

  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