Structure

Physi-Chem Properties

Molecular Weight:  166.11
Volume:  178.538
LogP:  2.229
LogD:  2.503
LogS:  -1.872
# Rotatable Bonds:  3
TPSA:  35.01
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.685
Synthetic Accessibility Score:  2.413
Fsp3:  0.556
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:  -4.312
MDCK Permeability:  3.8274043618002906e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.035

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.921
Plasma Protein Binding (PPB):  47.01255798339844%
Volume Distribution (VD):  1.398
Pgp-substrate:  43.36452102661133%

ADMET: Metabolism

CYP1A2-inhibitor:  0.515
CYP1A2-substrate:  0.636
CYP2C19-inhibitor:  0.193
CYP2C19-substrate:  0.91
CYP2C9-inhibitor:  0.071
CYP2C9-substrate:  0.935
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.711
CYP3A4-inhibitor:  0.03
CYP3A4-substrate:  0.261

ADMET: Excretion

Clearance (CL):  9.798
Half-life (T1/2):  0.603

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.378
Drug-inuced Liver Injury (DILI):  0.915
AMES Toxicity:  0.087
Rat Oral Acute Toxicity:  0.581
Maximum Recommended Daily Dose:  0.027
Skin Sensitization:  0.859
Carcinogencity:  0.301
Eye Corrosion:  0.026
Eye Irritation:  0.84
Respiratory Toxicity:  0.901

Download Data

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

  Natural Product: NPC215597

Natural Product ID:  NPC215597
Common Name*:   2-Methoxy-3-Isobutylpyrazine
IUPAC Name:   2-methoxy-3-(2-methylpropyl)pyrazine
Synonyms:  
Standard InCHIKey:  UXFSPRAGHGMRSQ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H14N2O/c1-7(2)6-8-9(12-3)11-5-4-10-8/h4-5,7H,6H2,1-3H3
SMILES:  CC(C)Cc1c(nccn1)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL97355
PubChem CID:   32594
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001346] Diazines
        • [CHEMONTID:0000067] Pyrazines
          • [CHEMONTID:0002563] Methoxypyrazines

*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
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[12932131]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[20460582]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[25172746]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[8910532]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16501 Capsicum annuum Species Solanaceae 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
NPT2 Others Unspecified Log 1/C = 7.472 n.a. PMID[494441]
NPT2 Others Unspecified Kd = 300.0 nM PMID[494442]

☑ 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 NPC215597 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
0.981 High Similarity NPC149621
0.6818 Remote Similarity NPC262236
0.6789 Remote Similarity NPC76536
0.6667 Remote Similarity NPC277608
0.6381 Remote Similarity NPC100312
0.6381 Remote Similarity NPC204104
0.6321 Remote Similarity NPC270637
0.6032 Remote Similarity NPC180417
0.5952 Remote Similarity NPC20249
0.5886 Remote Similarity NPC267928
0.5787 Remote Similarity NPC19872
0.5774 Remote Similarity NPC219963
0.5774 Remote Similarity NPC161887
0.5774 Remote Similarity NPC266551
0.5767 Remote Similarity NPC476518
0.5732 Remote Similarity NPC121658
0.5732 Remote Similarity NPC14651
0.5714 Remote Similarity NPC226202
0.5697 Remote Similarity NPC111624
0.5691 Remote Similarity NPC245816
0.5691 Remote Similarity NPC476138
0.5669 Remote Similarity NPC317307
0.5616 Remote Similarity NPC470140

  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 NPC215597 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
0.6261 Remote Similarity NPD8835 Approved
0.605 Remote Similarity NPD9101 Discontinued
0.5882 Remote Similarity NPD3576 Approved
0.5882 Remote Similarity NPD3575 Approved
0.5864 Remote Similarity NPD565 Phase 2
0.5772 Remote Similarity NPD9472 Phase 3
0.5705 Remote Similarity NPD9596 Approved
0.5705 Remote Similarity NPD9595 Approved
0.5687 Remote Similarity NPD1418 Phase 2
0.566 Remote Similarity NPD9574 Clinical (unspecified phase)
0.5655 Remote Similarity NPD715 Phase 3
0.5643 Remote Similarity NPD2225 Clinical (unspecified phase)
0.5607 Remote Similarity NPD1033 Clinical (unspecified phase)
0.5607 Remote Similarity NPD1034 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