Structure

Physi-Chem Properties

Molecular Weight:  80.04
Volume:  83.268
LogP:  -0.061
LogD:  -0.076
LogS:  0.848
# 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:  0.453
Synthetic Accessibility Score:  1.974
Fsp3:  0.0
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:  -3.992
MDCK Permeability:  4.704649836639874e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.026
Human Intestinal Absorption (HIA):  0.017
20% Bioavailability (F20%):  0.27
30% Bioavailability (F30%):  0.044

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.902
Plasma Protein Binding (PPB):  14.495285987854004%
Volume Distribution (VD):  1.172
Pgp-substrate:  85.90435028076172%

ADMET: Metabolism

CYP1A2-inhibitor:  0.206
CYP1A2-substrate:  0.587
CYP2C19-inhibitor:  0.191
CYP2C19-substrate:  0.557
CYP2C9-inhibitor:  0.045
CYP2C9-substrate:  0.151
CYP2D6-inhibitor:  0.258
CYP2D6-substrate:  0.094
CYP3A4-inhibitor:  0.164
CYP3A4-substrate:  0.308

ADMET: Excretion

Clearance (CL):  9.358
Half-life (T1/2):  0.715

ADMET: Toxicity

hERG Blockers:  0.04
Human Hepatotoxicity (H-HT):  0.111
Drug-inuced Liver Injury (DILI):  0.945
AMES Toxicity:  0.052
Rat Oral Acute Toxicity:  0.696
Maximum Recommended Daily Dose:  0.046
Skin Sensitization:  0.959
Carcinogencity:  0.091
Eye Corrosion:  0.981
Eye Irritation:  0.996
Respiratory Toxicity:  0.906

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

  Natural Product: NPC158948

Natural Product ID:  NPC158948
Common Name*:   Pyrazine
IUPAC Name:   pyrazine
Synonyms:   Pyrazine
Standard InCHIKey:  KYQCOXFCLRTKLS-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H4N2/c1-2-6-4-3-5-1/h1-4H
SMILES:  n1ccncc1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL15797
PubChem CID:   9261
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
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. PMID[19919095]
NPO21027 Daphnia magna Species Daphniidae Eukaryota n.a. n.a. n.a. PMID[20117838]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota leaves n.a. n.a. PMID[22272932]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota flower buds and leaves Khon Kaen province, Thailand 2010 PMID[23270663]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Leaves n.a. n.a. PMID[23642481]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[25320841]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Flowers n.a. n.a. PMID[26462418]
NPO21027 Daphnia magna Species Daphniidae Eukaryota n.a. n.a. n.a. Database[Article]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3478 Nelumbo nucifera Species Nelumbonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21027 Daphnia magna Species Daphniidae 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
NPT300 Individual Protein Thromboxane-A synthase Homo sapiens Inhibition = 12.0 % PMID[565051]
NPT2 Others Unspecified Potency n.a. 4473.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 160 nM PubChem BioAssay data set
NPT35 Others n.a. pKa = 0.4 n.a. PMID[565052]
NPT35 Others n.a. pKa = 0.7 n.a. PMID[565053]
NPT35 Others n.a. LogP = -0.26 n.a. PMID[565053]

☑ 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 NPC158948 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
0.7794 Intermediate Similarity NPC100312
0.7536 Intermediate Similarity NPC204104
0.7429 Intermediate Similarity NPC270637
0.6709 Remote Similarity NPC76536
0.6543 Remote Similarity NPC262236
0.6341 Remote Similarity NPC277608
0.5949 Remote Similarity NPC237936

  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 NPC158948 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
0.6386 Remote Similarity NPD8835 Approved
0.6092 Remote Similarity NPD9101 Discontinued
0.6076 Remote Similarity NPD8584 Approved
0.5949 Remote Similarity NPD8185 Discontinued
0.5949 Remote Similarity NPD8186 Phase 1
0.5889 Remote Similarity NPD9472 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