Structure

Physi-Chem Properties

Molecular Weight:  150.12
Volume:  169.748
LogP:  1.898
LogD:  1.964
LogS:  -0.814
# Rotatable Bonds:  2
TPSA:  25.78
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.643
Synthetic Accessibility Score:  2.439
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:  -4.558
MDCK Permeability:  2.825250521709677e-05
Pgp-inhibitor:  0.009
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.044

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.973
Plasma Protein Binding (PPB):  50.23675537109375%
Volume Distribution (VD):  1.444
Pgp-substrate:  42.56972885131836%

ADMET: Metabolism

CYP1A2-inhibitor:  0.87
CYP1A2-substrate:  0.942
CYP2C19-inhibitor:  0.032
CYP2C19-substrate:  0.658
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.13
CYP2D6-inhibitor:  0.149
CYP2D6-substrate:  0.581
CYP3A4-inhibitor:  0.026
CYP3A4-substrate:  0.413

ADMET: Excretion

Clearance (CL):  7.153
Half-life (T1/2):  0.534

ADMET: Toxicity

hERG Blockers:  0.026
Human Hepatotoxicity (H-HT):  0.166
Drug-inuced Liver Injury (DILI):  0.229
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.698
Maximum Recommended Daily Dose:  0.502
Skin Sensitization:  0.437
Carcinogencity:  0.404
Eye Corrosion:  0.037
Eye Irritation:  0.919
Respiratory Toxicity:  0.967

Download Data

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

  Natural Product: NPC277608

Natural Product ID:  NPC277608
Common Name*:   2,3-Diethyl-5-Methylpyrazine
IUPAC Name:   2,3-diethyl-5-methylpyrazine
Synonyms:  
Standard InCHIKey:  PSINWXIDJYEXLO-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H14N2/c1-4-8-9(5-2)11-7(3)6-10-8/h6H,4-5H2,1-3H3
SMILES:  CCc1nc(C)cnc1CC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1904383
PubChem CID:   28905
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
NPO21355 Elsholtzia ciliata Species Lamiaceae Eukaryota Aerial Parts n.a. n.a. PMID[32991171]
NPO21355 Elsholtzia ciliata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18046 Mosla chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18046 Mosla chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21355 Elsholtzia ciliata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21355 Elsholtzia ciliata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18046 Mosla chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18046 Mosla chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21355 Elsholtzia ciliata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18046 Mosla chinensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21355 Elsholtzia ciliata Species Lamiaceae 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
NPT135 Individual Protein Chromobox protein homolog 1 Homo sapiens Potency n.a. 2238.7 nM PMID[514589]
NPT10 Individual Protein Geminin Homo sapiens Potency n.a. 5.8 nM PMID[514589]
NPT49 Individual Protein DNA-(apurinic or apyrimidinic site) lyase Homo sapiens Potency n.a. 100.0 nM PMID[514589]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 18526.0 nM PMID[514589]

☑ 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 NPC277608 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
0.9756 High Similarity NPC262236
0.9512 High Similarity NPC76536
0.8519 High Similarity NPC270637
0.8395 Intermediate Similarity NPC204104
0.8171 Intermediate Similarity NPC100312
0.679 Remote Similarity NPC284039
0.679 Remote Similarity NPC229
0.6759 Remote Similarity NPC231655
0.6667 Remote Similarity NPC149621
0.6667 Remote Similarity NPC215597
0.6415 Remote Similarity NPC326248
0.6415 Remote Similarity NPC187191
0.6341 Remote Similarity NPC158948
0.6204 Remote Similarity NPC83987
0.6204 Remote Similarity NPC273327
0.6182 Remote Similarity NPC155498
0.6147 Remote Similarity NPC111132
0.614 Remote Similarity NPC27802
0.6018 Remote Similarity NPC76540
0.5984 Remote Similarity NPC182570
0.5984 Remote Similarity NPC265605
0.5984 Remote Similarity NPC48564
0.5932 Remote Similarity NPC143156
0.5887 Remote Similarity NPC46358
0.5872 Remote Similarity NPC213774
0.587 Remote Similarity NPC470111
0.587 Remote Similarity NPC201380
0.587 Remote Similarity NPC179787
0.5856 Remote Similarity NPC317307
0.5841 Remote Similarity NPC180417
0.5827 Remote Similarity NPC321911
0.5825 Remote Similarity NPC14223
0.5812 Remote Similarity NPC327613
0.5797 Remote Similarity NPC63545
0.5794 Remote Similarity NPC9639
0.5785 Remote Similarity NPC297486
0.5785 Remote Similarity NPC240136
0.5785 Remote Similarity NPC471402
0.5763 Remote Similarity NPC235843
0.576 Remote Similarity NPC290094
0.5755 Remote Similarity NPC469811
0.5738 Remote Similarity NPC91958
0.5714 Remote Similarity NPC473901
0.5714 Remote Similarity NPC27740
0.5672 Remote Similarity NPC251722
0.5672 Remote Similarity NPC314102
0.5669 Remote Similarity NPC146373
0.5669 Remote Similarity NPC245244
0.5669 Remote Similarity NPC166424
0.5649 Remote Similarity NPC256893
0.5625 Remote Similarity NPC202957
0.5625 Remote Similarity NPC169625
0.562 Remote Similarity NPC84268
0.561 Remote Similarity NPC143603

  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 NPC277608 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
0.7273 Intermediate Similarity NPD9472 Phase 3
0.679 Remote Similarity NPD9394 Clinical (unspecified phase)
0.6759 Remote Similarity NPD9099 Clinical (unspecified phase)
0.6759 Remote Similarity NPD9098 Phase 3
0.6609 Remote Similarity NPD9392 Approved
0.6609 Remote Similarity NPD9396 Approved
0.6585 Remote Similarity NPD715 Phase 3
0.6566 Remote Similarity NPD8835 Approved
0.6387 Remote Similarity NPD9598 Discontinued
0.6311 Remote Similarity NPD9101 Discontinued
0.624 Remote Similarity NPD9305 Clinical (unspecified phase)
0.623 Remote Similarity NPD9357 Approved
0.6183 Remote Similarity NPD174 Discontinued
0.6174 Remote Similarity NPD4824 Approved
0.6174 Remote Similarity NPD4823 Approved
0.616 Remote Similarity NPD1095 Clinical (unspecified phase)
0.6147 Remote Similarity NPD8861 Approved
0.6147 Remote Similarity NPD8859 Approved
0.6147 Remote Similarity NPD8862 Approved
0.6129 Remote Similarity NPD9583 Approved
0.608 Remote Similarity NPD2119 Approved
0.608 Remote Similarity NPD2118 Approved
0.6017 Remote Similarity NPD269 Clinical (unspecified phase)
0.6016 Remote Similarity NPD803 Phase 1
0.6016 Remote Similarity NPD809 Discontinued
0.6 Remote Similarity NPD1918 Clinical (unspecified phase)
0.5984 Remote Similarity NPD271 Approved
0.5984 Remote Similarity NPD270 Clinical (unspecified phase)
0.5984 Remote Similarity NPD268 Approved
0.5952 Remote Similarity NPD991 Phase 2
0.5952 Remote Similarity NPD992 Clinical (unspecified phase)
0.5938 Remote Similarity NPD3476 Approved
0.5938 Remote Similarity NPD3475 Approved
0.592 Remote Similarity NPD1807 Clinical (unspecified phase)
0.5897 Remote Similarity NPD757 Phase 3
0.5802 Remote Similarity NPD3944 Approved
0.5802 Remote Similarity NPD3942 Approved
0.5802 Remote Similarity NPD4030 Approved
0.5802 Remote Similarity NPD4029 Approved
0.5802 Remote Similarity NPD4028 Approved
0.5776 Remote Similarity NPD9082 Approved
0.5726 Remote Similarity NPD1390 Phase 1
0.5726 Remote Similarity NPD1389 Clinical (unspecified phase)
0.5726 Remote Similarity NPD1388 Phase 1
0.5714 Remote Similarity NPD3576 Approved
0.5714 Remote Similarity NPD3575 Approved
0.5714 Remote Similarity NPD9132 Discontinued
0.568 Remote Similarity NPD5787 Discontinued
0.5645 Remote Similarity NPD4811 Discontinued
0.5643 Remote Similarity NPD1661 Suspended

  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