Structure

Physi-Chem Properties

Molecular Weight:  128.06
Volume:  120.781
LogP:  -1.125
LogD:  -0.961
LogS:  -0.936
# Rotatable Bonds:  0
TPSA:  58.2
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.422
Synthetic Accessibility Score:  3.16
Fsp3:  0.6
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:  -5.321
MDCK Permeability:  9.373626198794227e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.094
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.997
Plasma Protein Binding (PPB):  7.800278186798096%
Volume Distribution (VD):  0.696
Pgp-substrate:  88.14586639404297%

ADMET: Metabolism

CYP1A2-inhibitor:  0.013
CYP1A2-substrate:  0.092
CYP2C19-inhibitor:  0.034
CYP2C19-substrate:  0.074
CYP2C9-inhibitor:  0.03
CYP2C9-substrate:  0.073
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.136
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.077

ADMET: Excretion

Clearance (CL):  4.003
Half-life (T1/2):  0.686

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.058
Drug-inuced Liver Injury (DILI):  0.027
AMES Toxicity:  0.012
Rat Oral Acute Toxicity:  0.026
Maximum Recommended Daily Dose:  0.018
Skin Sensitization:  0.25
Carcinogencity:  0.009
Eye Corrosion:  0.004
Eye Irritation:  0.036
Respiratory Toxicity:  0.125

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

  Natural Product: NPC25237

Natural Product ID:  NPC25237
Common Name*:   (S)-3-Methylpiperazine-2,5-Dione
IUPAC Name:   (3S)-3-methylpiperazine-2,5-dione
Synonyms:  
Standard InCHIKey:  ICCHEGCKVBMSTF-VKHMYHEASA-N
Standard InCHI:  InChI=1S/C5H8N2O2/c1-3-5(9)6-2-4(8)7-3/h3H,2H2,1H3,(H,6,9)(H,7,8)/t3-/m0/s1
SMILES:  OC1=N[C@H](C(=NC1)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2229111
PubChem CID:   7408474
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and 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
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17616609]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17929896]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19113967]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19159274]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19256529]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. isolated from sediment collected using a hand held deep water sampling device at >33 m depth in Vanuatu 2003 PMID[20303767]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21667925]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21954885]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22106303]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota stem bark of Melia azedarach n.a. n.a. PMID[22409377]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23557488]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23563483]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[7622436]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10538 Aspergillus fumigatus Species Aspergillaceae 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
NPT176 Organism Artemia salina Artemia salina LC50 > 100.0 ug.mL-1 PMID[522997]

☑ 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 NPC25237 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
0.7727 Intermediate Similarity NPC180402
0.7727 Intermediate Similarity NPC87359
0.7083 Intermediate Similarity NPC137327
0.7 Intermediate Similarity NPC150560
0.6889 Remote Similarity NPC297220
0.6667 Remote Similarity NPC327250
0.6458 Remote Similarity NPC80350
0.641 Remote Similarity NPC328698
0.617 Remote Similarity NPC248970
0.617 Remote Similarity NPC306238
0.6122 Remote Similarity NPC328378
0.6 Remote Similarity NPC327239
0.6 Remote Similarity NPC319175
0.6 Remote Similarity NPC260324
0.6 Remote Similarity NPC145895
0.5962 Remote Similarity NPC321118
0.5962 Remote Similarity NPC316889
0.5918 Remote Similarity NPC227850
0.5882 Remote Similarity NPC318463
0.5849 Remote Similarity NPC322573
0.5814 Remote Similarity NPC69179
0.5789 Remote Similarity NPC254685
0.5769 Remote Similarity NPC329495
0.5741 Remote Similarity NPC38463
0.5714 Remote Similarity NPC319709
0.5714 Remote Similarity NPC289484
0.569 Remote Similarity NPC243964
0.5686 Remote Similarity NPC224624
0.5682 Remote Similarity NPC111686
0.5667 Remote Similarity NPC84182
0.5667 Remote Similarity NPC128005
0.5652 Remote Similarity NPC241279
0.5652 Remote Similarity NPC105488
0.56 Remote Similarity NPC153370

  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 NPC25237 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
0.7727 Intermediate Similarity NPD362 Phase 1
0.7222 Intermediate Similarity NPD8613 Approved
0.7105 Intermediate Similarity NPD8572 Approved
0.617 Remote Similarity NPD8870 Approved
0.6087 Remote Similarity NPD9400 Approved
0.6087 Remote Similarity NPD8869 Approved
0.6087 Remote Similarity NPD9399 Approved
0.6042 Remote Similarity NPD379 Clinical (unspecified phase)
0.6 Remote Similarity NPD329 Discontinued
0.5926 Remote Similarity NPD583 Approved
0.5926 Remote Similarity NPD843 Clinical (unspecified phase)
0.5926 Remote Similarity NPD581 Approved
0.5926 Remote Similarity NPD584 Approved
0.5918 Remote Similarity NPD9213 Approved
0.5918 Remote Similarity NPD9214 Phase 3
0.5849 Remote Similarity NPD1830 Clinical (unspecified phase)
0.5833 Remote Similarity NPD1152 Phase 2
0.5789 Remote Similarity NPD8622 Discontinued
0.5714 Remote Similarity NPD3211 Approved
0.566 Remote Similarity NPD9419 Clinical (unspecified phase)
0.5652 Remote Similarity NPD8198 Approved
0.5652 Remote Similarity NPD8197 Approved
0.5625 Remote Similarity NPD397 Phase 2
0.56 Remote Similarity NPD8614 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