Structure

Physi-Chem Properties

Molecular Weight:  253.17
Volume:  271.602
LogP:  4.727
LogD:  3.975
LogS:  -3.352
# Rotatable Bonds:  9
TPSA:  73.32
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.463
Synthetic Accessibility Score:  2.581
Fsp3:  0.643
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.789
MDCK Permeability:  2.4150651370291598e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.999
30% Bioavailability (F30%):  0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.697
Plasma Protein Binding (PPB):  96.14019775390625%
Volume Distribution (VD):  0.668
Pgp-substrate:  3.4376285076141357%

ADMET: Metabolism

CYP1A2-inhibitor:  0.924
CYP1A2-substrate:  0.512
CYP2C19-inhibitor:  0.854
CYP2C19-substrate:  0.065
CYP2C9-inhibitor:  0.696
CYP2C9-substrate:  0.962
CYP2D6-inhibitor:  0.882
CYP2D6-substrate:  0.433
CYP3A4-inhibitor:  0.601
CYP3A4-substrate:  0.096

ADMET: Excretion

Clearance (CL):  4.796
Half-life (T1/2):  0.686

ADMET: Toxicity

hERG Blockers:  0.028
Human Hepatotoxicity (H-HT):  0.23
Drug-inuced Liver Injury (DILI):  0.92
AMES Toxicity:  0.08
Rat Oral Acute Toxicity:  0.815
Maximum Recommended Daily Dose:  0.031
Skin Sensitization:  0.799
Carcinogencity:  0.126
Eye Corrosion:  0.012
Eye Irritation:  0.88
Respiratory Toxicity:  0.876

Download Data

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

  Natural Product: NPC469836

Natural Product ID:  NPC469836
Common Name*:   3-Decanoyll Tetramic Acid
IUPAC Name:   (3Z)-3-(1-hydroxydecylidene)pyrrolidine-2,4-dione
Synonyms:  
Standard InCHIKey:  USWXONDRQANYOY-QBFSEMIESA-N
Standard InCHI:  InChI=1S/C14H23NO3/c1-2-3-4-5-6-7-8-9-11(16)13-12(17)10-15-14(13)18/h16H,2-10H2,1H3,(H,15,18)/b13-11-
SMILES:  CCCCCCCCC/C(=C/1C(=O)CN=C1O)/O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1213028
PubChem CID:   54726231
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines
        • [CHEMONTID:0001158] Pyrrolidones
          • [CHEMONTID:0003032] Pyrrolidine-3-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
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[10556916]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[19406895]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[19917748]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[20932054]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[25043228]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[25960261]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[32603106]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. Antarctic n.a. PMID[8882433]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria 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
NPT2940 Organism Clostridium difficile Clostridium difficile FC = 100000.0 n.a. PMID[510132]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 100000.0 nM PMID[510133]
NPT2 Others Unspecified IC50 = 30000.0 nM PMID[510133]

☑ 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 NPC469836 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
0.9706 High Similarity NPC469835
0.8684 High Similarity NPC469838
0.8684 High Similarity NPC469833
0.7945 Intermediate Similarity NPC4706
0.7215 Intermediate Similarity NPC263266
0.6562 Remote Similarity NPC175531
0.6562 Remote Similarity NPC313234
0.6429 Remote Similarity NPC474563
0.6389 Remote Similarity NPC40148
0.6353 Remote Similarity NPC477485
0.631 Remote Similarity NPC46268
0.631 Remote Similarity NPC477484
0.631 Remote Similarity NPC477486
0.6286 Remote Similarity NPC476814
0.6286 Remote Similarity NPC476813
0.6176 Remote Similarity NPC307903
0.6176 Remote Similarity NPC140251
0.6117 Remote Similarity NPC24389
0.6104 Remote Similarity NPC316674
0.6081 Remote Similarity NPC192843
0.6076 Remote Similarity NPC187315
0.6058 Remote Similarity NPC476290
0.6053 Remote Similarity NPC130807
0.6053 Remote Similarity NPC6795
0.6 Remote Similarity NPC469598
0.5974 Remote Similarity NPC29468
0.5955 Remote Similarity NPC473810
0.5946 Remote Similarity NPC469515
0.5943 Remote Similarity NPC476269
0.5926 Remote Similarity NPC249713
0.5914 Remote Similarity NPC34754
0.5882 Remote Similarity NPC472616
0.5867 Remote Similarity NPC281230
0.5867 Remote Similarity NPC245650
0.5854 Remote Similarity NPC280065
0.5854 Remote Similarity NPC291196
0.5854 Remote Similarity NPC471022
0.5854 Remote Similarity NPC45060
0.5854 Remote Similarity NPC103712
0.5833 Remote Similarity NPC144419
0.5816 Remote Similarity NPC175614
0.5806 Remote Similarity NPC472614
0.5795 Remote Similarity NPC471597
0.5789 Remote Similarity NPC469494
0.5769 Remote Similarity NPC273614
0.5765 Remote Similarity NPC7382
0.5761 Remote Similarity NPC319913
0.5758 Remote Similarity NPC4834
0.5729 Remote Similarity NPC472264
0.5727 Remote Similarity NPC476190
0.5714 Remote Similarity NPC312826
0.5714 Remote Similarity NPC471595
0.5714 Remote Similarity NPC329003
0.5714 Remote Similarity NPC325550
0.5714 Remote Similarity NPC106309
0.5714 Remote Similarity NPC326524
0.5699 Remote Similarity NPC322672
0.5698 Remote Similarity NPC89374
0.5698 Remote Similarity NPC476924
0.5698 Remote Similarity NPC476923
0.5686 Remote Similarity NPC128501
0.5673 Remote Similarity NPC472615
0.5641 Remote Similarity NPC309877
0.5638 Remote Similarity NPC473525
0.5632 Remote Similarity NPC182848
0.5618 Remote Similarity NPC258231
0.5612 Remote Similarity NPC116930
0.5604 Remote Similarity NPC474312
0.56 Remote Similarity NPC273023

  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 NPC469836 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
NPD

  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