Structure

Physi-Chem Properties

Molecular Weight:  99.03
Volume:  92.488
LogP:  0.081
LogD:  0.562
LogS:  -1.39
# Rotatable Bonds:  0
TPSA:  56.25
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.441
Synthetic Accessibility Score:  3.817
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:  -5.096
MDCK Permeability:  8.381885891139973e-06
Pgp-inhibitor:  0.001
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  0.937
30% Bioavailability (F30%):  0.502

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.066
Plasma Protein Binding (PPB):  27.135927200317383%
Volume Distribution (VD):  0.976
Pgp-substrate:  70.60367584228516%

ADMET: Metabolism

CYP1A2-inhibitor:  0.017
CYP1A2-substrate:  0.188
CYP2C19-inhibitor:  0.034
CYP2C19-substrate:  0.054
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.921
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.719
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.081

ADMET: Excretion

Clearance (CL):  11.409
Half-life (T1/2):  0.881

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.193
Drug-inuced Liver Injury (DILI):  0.492
AMES Toxicity:  0.186
Rat Oral Acute Toxicity:  0.658
Maximum Recommended Daily Dose:  0.007
Skin Sensitization:  0.094
Carcinogencity:  0.703
Eye Corrosion:  0.341
Eye Irritation:  0.654
Respiratory Toxicity:  0.717

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

  Natural Product: NPC33721

Natural Product ID:  NPC33721
Common Name*:   Succinimide
IUPAC Name:   pyrrolidine-2,5-dione
Synonyms:   Succinimide
Standard InCHIKey:  KZNICNPSHKQLFF-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H5NO2/c6-3-1-2-4(7)5-3/h1-2H2,(H,5,6,7)
SMILES:  OC1=NC(=O)CC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL275661
PubChem CID:   11439
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines
        • [CHEMONTID:0001158] Pyrrolidones
          • [CHEMONTID:0003031] Pyrrolidine-2-ones

*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
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[10075755]
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[11000019]
NPO11248 Tachigalia paniculata n.a. n.a. n.a. leaves n.a. n.a. PMID[12444671]
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]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. leaf n.a. PMID[18409045]
NPO29141 Panax ginseng Species Araliaceae Eukaryota flower buds n.a. n.a. PMID[19926279]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. PMID[2026709]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. root n.a. PMID[2092947]
NPO29141 Panax ginseng Species Araliaceae Eukaryota berry n.a. n.a. PMID[21216145]
NPO29141 Panax ginseng Species Araliaceae Eukaryota leaves n.a. n.a. PMID[24290061]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[24968750]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[25152999]
NPO2494 Xanthium strumarium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[26081757]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota Steamed Roots n.a. n.a. PMID[26200131]
NPO29141 Panax ginseng Species Araliaceae Eukaryota stems-leaves n.a. n.a. PMID[26420067]
NPO2494 Xanthium strumarium Species Asteraceae Eukaryota n.a. aerial part n.a. PMID[27169184]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. stem n.a. PMID[27914541]
NPO29141 Panax ginseng Species Araliaceae Eukaryota Flower Buds n.a. n.a. PMID[28345906]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18030 Herba acalyphae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng 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[TCM_Taiwan]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2494 Xanthium strumarium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2494 Xanthium strumarium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14255 Streptomyces flocculus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO11642 Dacrydium cupressinum Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21891 Panax notoginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19635 Coreopsis nodosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12684 Trigonella grandiflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7998 Senecio paludaffinis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22666 Haematococcus lacustris Species Haematococcaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13568 Hypoxylon rubiginosum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13166 Nicotiana undulata Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11248 Tachigalia paniculata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO731 Panax schinseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5189 Glycine tomentella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12001 Saccharomyces pastori Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11488 Alstonia muelleriana Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21854 Pterocladiella tenuis Species Gelidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14354 Artemisia cina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18805 Tripolium pannonicum Species Asteraceae 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
NPT2607 Individual Protein Cereblon isoform 4 Magnetospirillum gryphiswaldense IC50 = 7600.0 nM PMID[450226]
NPT2608 Individual Protein Protein cereblon Homo sapiens IC50 = 34500.0 nM PMID[450226]
NPT2607 Individual Protein Cereblon isoform 4 Magnetospirillum gryphiswaldense IC50 = 53000.0 nM PMID[450226]
NPT2607 Individual Protein Cereblon isoform 4 Magnetospirillum gryphiswaldense Ki = 4300.0 nM PMID[450226]
NPT2608 Individual Protein Protein cereblon Homo sapiens Ki = 26200.0 nM PMID[450226]
NPT2607 Individual Protein Cereblon isoform 4 Magnetospirillum gryphiswaldense Ki = 47800.0 nM PMID[450226]
NPT2607 Individual Protein Cereblon isoform 4 Magnetospirillum gryphiswaldense Ki = 4300.0 nM PMID[450227]
NPT2608 Individual Protein Protein cereblon Homo sapiens IC50 = 22300.0 nM PMID[450228]
NPT2608 Individual Protein Protein cereblon Homo sapiens Ki = 8190.0 nM PMID[450228]
NPT2607 Individual Protein Cereblon isoform 4 Magnetospirillum gryphiswaldense Ki = 642.0 nM PMID[450228]
NPT2607 Individual Protein Cereblon isoform 4 Magnetospirillum gryphiswaldense IC50 = 3530.0 nM PMID[450228]
NPT32 Organism Mus musculus Mus musculus Inhibition = 2.0 % PMID[450222]
NPT32 Organism Mus musculus Mus musculus Inhibition = 27.0 % PMID[450222]
NPT32 Organism Mus musculus Mus musculus Inhibition = 32.0 % PMID[450222]
NPT1572 Protein Family Glycogen synthase kinase-3 Homo sapiens IC50 > 100000.0 nM PMID[450223]
NPT35 Others n.a. LogP = -2.31 n.a. PMID[450225]
NPT35 Others n.a. LogP = -1.51 n.a. PMID[450225]
NPT2 Others Unspecified IC50 = 6700.0 nM PMID[450226]
NPT2 Others Unspecified Ki = 5800.0 nM PMID[450226]

☑ 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 NPC33721 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
0.8 Intermediate Similarity NPC21142
0.7368 Intermediate Similarity NPC145895
0.66 Remote Similarity NPC29950
0.66 Remote Similarity NPC19576
0.6486 Remote Similarity NPC290188
0.6078 Remote Similarity NPC327239
0.5962 Remote Similarity NPC471131
0.5833 Remote Similarity NPC43264
0.5789 Remote Similarity NPC292299
0.5789 Remote Similarity NPC34838
0.569 Remote Similarity NPC263207

  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 NPC33721 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
1.0 High Similarity NPD8576 Approved
0.8 Intermediate Similarity NPD9200 Approved
0.66 Remote Similarity NPD8846 Approved
0.66 Remote Similarity NPD61 Approved
0.66 Remote Similarity NPD8847 Approved
0.6042 Remote Similarity NPD9658 Clinical (unspecified phase)
0.5952 Remote Similarity NPD8572 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