Structure

Physi-Chem Properties

Molecular Weight:  184.12
Volume:  189.965
LogP:  0.797
LogD:  1.129
LogS:  -1.565
# Rotatable Bonds:  2
TPSA:  58.2
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.636
Synthetic Accessibility Score:  3.171
Fsp3:  0.778
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:  -4.853
MDCK Permeability:  1.9118595446343534e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.063
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.915
Plasma Protein Binding (PPB):  11.256509780883789%
Volume Distribution (VD):  0.699
Pgp-substrate:  74.3724136352539%

ADMET: Metabolism

CYP1A2-inhibitor:  0.027
CYP1A2-substrate:  0.096
CYP2C19-inhibitor:  0.044
CYP2C19-substrate:  0.184
CYP2C9-inhibitor:  0.03
CYP2C9-substrate:  0.148
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.15
CYP3A4-inhibitor:  0.026
CYP3A4-substrate:  0.177

ADMET: Excretion

Clearance (CL):  5.39
Half-life (T1/2):  0.661

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.241
Drug-inuced Liver Injury (DILI):  0.066
AMES Toxicity:  0.054
Rat Oral Acute Toxicity:  0.076
Maximum Recommended Daily Dose:  0.022
Skin Sensitization:  0.088
Carcinogencity:  0.033
Eye Corrosion:  0.004
Eye Irritation:  0.038
Respiratory Toxicity:  0.048

Download Data

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

  Natural Product: NPC87359

Natural Product ID:  NPC87359
Common Name*:   (3S,6S)-3-Isobutyl-6-Methylpiperazine-2,5-Dione
IUPAC Name:   (3S,6S)-3-methyl-6-(2-methylpropyl)piperazine-2,5-dione
Synonyms:  
Standard InCHIKey:  DBJPZCJQDRPOME-BQBZGAKWSA-N
Standard InCHI:  InChI=1S/C9H16N2O2/c1-5(2)4-7-9(13)10-6(3)8(12)11-7/h5-7H,4H2,1-3H3,(H,10,13)(H,11,12)/t6-,7-/m0/s1
SMILES:  CC(C[C@@H]1N=C(O)[C@@H](N=C1O)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1957401
PubChem CID:   13879946
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
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Flower buds n.a. n.a. PMID[12880307]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Stems n.a. n.a. PMID[17663584]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Roots n.a. n.a. PMID[18186611]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Steamed Roots n.a. n.a. PMID[26200131]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21891 Panax notoginseng Species Araliaceae 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Inhibition = 0.0 % PMID[485077]

☑ 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 NPC87359 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
1.0 High Similarity NPC180402
0.9167 High Similarity NPC137327
0.8542 High Similarity NPC80350
0.7727 Intermediate Similarity NPC25237
0.7321 Intermediate Similarity NPC472578
0.7193 Intermediate Similarity NPC327748
0.7193 Intermediate Similarity NPC321468
0.717 Intermediate Similarity NPC322946
0.7143 Intermediate Similarity NPC317147
0.7069 Intermediate Similarity NPC327170
0.7069 Intermediate Similarity NPC329564
0.6957 Remote Similarity NPC150560
0.6949 Remote Similarity NPC314510
0.6897 Remote Similarity NPC317143
0.6897 Remote Similarity NPC316826
0.6842 Remote Similarity NPC318260
0.6613 Remote Similarity NPC41429
0.6607 Remote Similarity NPC316889
0.6607 Remote Similarity NPC321118
0.6567 Remote Similarity NPC161774
0.6567 Remote Similarity NPC266888
0.6567 Remote Similarity NPC256312
0.6545 Remote Similarity NPC471131
0.6515 Remote Similarity NPC196007
0.6515 Remote Similarity NPC214532
0.6515 Remote Similarity NPC76297
0.6324 Remote Similarity NPC209156
0.625 Remote Similarity NPC470108
0.6212 Remote Similarity NPC472579
0.6182 Remote Similarity NPC328378
0.6154 Remote Similarity NPC470109
0.6119 Remote Similarity NPC478256
0.6111 Remote Similarity NPC312315
0.6111 Remote Similarity NPC289484
0.6111 Remote Similarity NPC319709
0.6078 Remote Similarity NPC241279
0.6071 Remote Similarity NPC327239
0.6066 Remote Similarity NPC254541
0.6061 Remote Similarity NPC195165
0.6061 Remote Similarity NPC470110
0.6034 Remote Similarity NPC270041
0.6 Remote Similarity NPC84182
0.6 Remote Similarity NPC128005
0.6 Remote Similarity NPC327250
0.5946 Remote Similarity NPC470783
0.5938 Remote Similarity NPC313420
0.5932 Remote Similarity NPC322573
0.5902 Remote Similarity NPC189301
0.5902 Remote Similarity NPC176164
0.5882 Remote Similarity NPC476285
0.5857 Remote Similarity NPC43219
0.5833 Remote Similarity NPC38463
0.5806 Remote Similarity NPC321536
0.5806 Remote Similarity NPC320598
0.58 Remote Similarity NPC111686
0.5797 Remote Similarity NPC477200
0.5789 Remote Similarity NPC329181
0.5789 Remote Similarity NPC224624
0.5789 Remote Similarity NPC224072
0.5789 Remote Similarity NPC319110
0.5781 Remote Similarity NPC243964
0.5781 Remote Similarity NPC327252
0.5781 Remote Similarity NPC124849
0.5781 Remote Similarity NPC21848
0.5775 Remote Similarity NPC86064
0.5714 Remote Similarity NPC315897
0.5714 Remote Similarity NPC143722
0.5652 Remote Similarity NPC476291
0.5636 Remote Similarity NPC297220
0.5634 Remote Similarity NPC138435
0.5616 Remote Similarity NPC472594
0.5614 Remote Similarity NPC245027
0.5614 Remote Similarity NPC162620
0.5614 Remote Similarity NPC62045

  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 NPC87359 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
0.8723 High Similarity NPD362 Phase 1
0.7755 Intermediate Similarity NPD379 Clinical (unspecified phase)
0.7407 Intermediate Similarity NPD1830 Clinical (unspecified phase)
0.717 Intermediate Similarity NPD9441 Phase 2
0.6981 Remote Similarity NPD325 Approved
0.6792 Remote Similarity NPD323 Approved
0.6727 Remote Similarity NPD611 Approved
0.6727 Remote Similarity NPD609 Approved
0.6667 Remote Similarity NPD324 Approved
0.661 Remote Similarity NPD354 Approved
0.6607 Remote Similarity NPD610 Approved
0.6607 Remote Similarity NPD608 Approved
0.6607 Remote Similarity NPD606 Approved
0.6607 Remote Similarity NPD607 Approved
0.6471 Remote Similarity NPD9400 Approved
0.6471 Remote Similarity NPD9399 Approved
0.6349 Remote Similarity NPD1831 Phase 3
0.6327 Remote Similarity NPD9453 Phase 3
0.6271 Remote Similarity NPD9647 Approved
0.6226 Remote Similarity NPD1152 Phase 2
0.6212 Remote Similarity NPD3724 Clinical (unspecified phase)
0.6176 Remote Similarity NPD3187 Discontinued
0.6154 Remote Similarity NPD2263 Discontinued
0.6111 Remote Similarity NPD3211 Approved
0.6071 Remote Similarity NPD903 Approved
0.6066 Remote Similarity NPD570 Approved
0.5968 Remote Similarity NPD571 Approved
0.5942 Remote Similarity NPD1147 Phase 2
0.5902 Remote Similarity NPD9433 Approved
0.5873 Remote Similarity NPD574 Approved
0.5867 Remote Similarity NPD2683 Discontinued
0.5781 Remote Similarity NPD575 Clinical (unspecified phase)
0.5781 Remote Similarity NPD834 Approved
0.5781 Remote Similarity NPD835 Approved
0.5741 Remote Similarity NPD9658 Clinical (unspecified phase)
0.5738 Remote Similarity NPD273 Approved
0.5735 Remote Similarity NPD620 Approved
0.5714 Remote Similarity NPD1825 Clinical (unspecified phase)
0.5692 Remote Similarity NPD832 Approved
0.5692 Remote Similarity NPD833 Approved
0.5667 Remote Similarity NPD9652 Approved
0.5652 Remote Similarity NPD8613 Approved
0.5652 Remote Similarity NPD8794 Clinical (unspecified phase)
0.5625 Remote Similarity NPD8572 Approved
0.5616 Remote Similarity NPD2689 Clinical (unspecified phase)
0.5614 Remote Similarity NPD9018 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