Structure

Physi-Chem Properties

Molecular Weight:  297.19
Volume:  314.984
LogP:  4.313
LogD:  3.11
LogS:  -3.681
# Rotatable Bonds:  11
TPSA:  93.55
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.372
Synthetic Accessibility Score:  2.762
Fsp3:  0.688
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.94
MDCK Permeability:  2.347308509342838e-05
Pgp-inhibitor:  0.021
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.021
20% Bioavailability (F20%):  0.996
30% Bioavailability (F30%):  0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.659
Plasma Protein Binding (PPB):  95.49227142333984%
Volume Distribution (VD):  0.81
Pgp-substrate:  2.3950319290161133%

ADMET: Metabolism

CYP1A2-inhibitor:  0.799
CYP1A2-substrate:  0.691
CYP2C19-inhibitor:  0.4
CYP2C19-substrate:  0.056
CYP2C9-inhibitor:  0.556
CYP2C9-substrate:  0.906
CYP2D6-inhibitor:  0.798
CYP2D6-substrate:  0.255
CYP3A4-inhibitor:  0.302
CYP3A4-substrate:  0.097

ADMET: Excretion

Clearance (CL):  4.419
Half-life (T1/2):  0.813

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.198
Drug-inuced Liver Injury (DILI):  0.909
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.197
Maximum Recommended Daily Dose:  0.018
Skin Sensitization:  0.783
Carcinogencity:  0.155
Eye Corrosion:  0.003
Eye Irritation:  0.183
Respiratory Toxicity:  0.912

Download Data

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

  Natural Product: NPC469833

Natural Product ID:  NPC469833
Common Name*:   OSWGMRUTKTWVOY-HUTFPVNGSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OSWGMRUTKTWVOY-HUTFPVNGSA-N
Standard InCHI:  InChI=1S/C16H27NO4/c1-2-3-4-5-6-7-8-9-13(19)14-15(20)12(10-11-18)17-16(14)21/h12,18-19H,2-11H2,1H3,(H,17,21)/b14-13-/t12-/m1/s1
SMILES:  CCCCCCCCC/C(=C1/C(=N[C@@H](C1=O)CCO)O)/O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1213025
PubChem CID:   n.a.
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
NPT2 Others Unspecified IC50 = 28000.0 nM PMID[523530]

☑ 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 NPC469833 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 NPC469838
0.8947 High Similarity NPC469835
0.8684 High Similarity NPC469836
0.7407 Intermediate Similarity NPC4706
0.7245 Intermediate Similarity NPC313234
0.6931 Remote Similarity NPC474563
0.6827 Remote Similarity NPC140251
0.6827 Remote Similarity NPC307903
0.6759 Remote Similarity NPC476814
0.6759 Remote Similarity NPC476813
0.6569 Remote Similarity NPC175531
0.6538 Remote Similarity NPC472616
0.6449 Remote Similarity NPC24389
0.642 Remote Similarity NPC29468
0.641 Remote Similarity NPC40148
0.6404 Remote Similarity NPC263266
0.6389 Remote Similarity NPC476290
0.6321 Remote Similarity NPC472615
0.6289 Remote Similarity NPC34754
0.6279 Remote Similarity NPC103712
0.6279 Remote Similarity NPC291196
0.6273 Remote Similarity NPC476269
0.6262 Remote Similarity NPC475800
0.6261 Remote Similarity NPC469515
0.6239 Remote Similarity NPC469494
0.6196 Remote Similarity NPC477485
0.619 Remote Similarity NPC469598
0.618 Remote Similarity NPC288086
0.6176 Remote Similarity NPC175614
0.617 Remote Similarity NPC474312
0.6154 Remote Similarity NPC477484
0.6154 Remote Similarity NPC477486
0.6147 Remote Similarity NPC474725
0.6147 Remote Similarity NPC133729
0.6136 Remote Similarity NPC320865
0.6136 Remote Similarity NPC477641
0.6136 Remote Similarity NPC477643
0.6117 Remote Similarity NPC167380
0.6098 Remote Similarity NPC130807
0.6092 Remote Similarity NPC471022
0.6092 Remote Similarity NPC477642
0.6092 Remote Similarity NPC45060
0.6092 Remote Similarity NPC280065
0.6091 Remote Similarity NPC113012
0.6091 Remote Similarity NPC122926
0.6067 Remote Similarity NPC144419
0.6053 Remote Similarity NPC476190
0.5979 Remote Similarity NPC307126
0.5979 Remote Similarity NPC68303
0.5978 Remote Similarity NPC46268
0.5962 Remote Similarity NPC4834
0.5957 Remote Similarity NPC47653
0.5943 Remote Similarity NPC474873
0.5941 Remote Similarity NPC472264
0.5934 Remote Similarity NPC264417
0.5934 Remote Similarity NPC217095
0.5909 Remote Similarity NPC236208
0.5905 Remote Similarity NPC234542
0.59 Remote Similarity NPC159369
0.59 Remote Similarity NPC39290
0.5893 Remote Similarity NPC170375
0.5889 Remote Similarity NPC314678
0.5888 Remote Similarity NPC128501
0.5877 Remote Similarity NPC471645
0.5873 Remote Similarity NPC328070
0.5865 Remote Similarity NPC121857
0.5859 Remote Similarity NPC472614
0.5851 Remote Similarity NPC258231
0.5849 Remote Similarity NPC473224
0.5841 Remote Similarity NPC469865
0.5841 Remote Similarity NPC7797
0.5833 Remote Similarity NPC476877
0.5825 Remote Similarity NPC116930
0.5824 Remote Similarity NPC227396
0.5816 Remote Similarity NPC319913
0.5814 Remote Similarity NPC477525
0.581 Remote Similarity NPC265662
0.5806 Remote Similarity NPC473536
0.5804 Remote Similarity NPC127578
0.5795 Remote Similarity NPC249713
0.5789 Remote Similarity NPC91332
0.5789 Remote Similarity NPC162741
0.5783 Remote Similarity NPC329003
0.5783 Remote Similarity NPC326524
0.5783 Remote Similarity NPC325550
0.5773 Remote Similarity NPC185256
0.5769 Remote Similarity NPC150041
0.5766 Remote Similarity NPC475150
0.5765 Remote Similarity NPC145658
0.5761 Remote Similarity NPC476924
0.5758 Remote Similarity NPC322672
0.575 Remote Similarity NPC16709
0.5747 Remote Similarity NPC187315
0.5732 Remote Similarity NPC192843
0.5729 Remote Similarity NPC82799
0.5727 Remote Similarity NPC472433
0.5727 Remote Similarity NPC476876
0.5726 Remote Similarity NPC296361
0.5714 Remote Similarity NPC298484
0.5714 Remote Similarity NPC6795
0.5701 Remote Similarity NPC233932
0.57 Remote Similarity NPC473525
0.5699 Remote Similarity NPC256640
0.5699 Remote Similarity NPC205615
0.5699 Remote Similarity NPC16279
0.5692 Remote Similarity NPC473052
0.5692 Remote Similarity NPC473055
0.5691 Remote Similarity NPC329919
0.5691 Remote Similarity NPC477793
0.5676 Remote Similarity NPC251330
0.567 Remote Similarity NPC477487
0.567 Remote Similarity NPC473810
0.5663 Remote Similarity NPC321030
0.566 Remote Similarity NPC476344
0.5652 Remote Similarity NPC5485
0.5649 Remote Similarity NPC322526
0.5648 Remote Similarity NPC188785
0.5648 Remote Similarity NPC77703
0.5648 Remote Similarity NPC316250
0.5641 Remote Similarity NPC216335
0.5641 Remote Similarity NPC316325
0.5636 Remote Similarity NPC74035
0.5636 Remote Similarity NPC14537
0.5631 Remote Similarity NPC314500
0.5625 Remote Similarity NPC217188
0.5618 Remote Similarity NPC28348
0.5618 Remote Similarity NPC477452
0.5618 Remote Similarity NPC474299
0.5618 Remote Similarity NPC475808
0.5618 Remote Similarity NPC474298
0.5618 Remote Similarity NPC473985
0.5612 Remote Similarity NPC471595
0.5603 Remote Similarity NPC50694

  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 NPC469833 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
0.6136 Remote Similarity NPD2256 Clinical (unspecified phase)
0.5946 Remote Similarity NPD6420 Discontinued
0.5929 Remote Similarity NPD1376 Discontinued
0.5893 Remote Similarity NPD7601 Clinical (unspecified phase)
0.5856 Remote Similarity NPD6413 Approved
0.5854 Remote Similarity NPD6914 Discontinued
0.5747 Remote Similarity NPD3704 Approved
0.5714 Remote Similarity NPD4228 Discovery
0.5641 Remote Similarity NPD7500 Approved
0.5614 Remote Similarity NPD7116 Clinical (unspecified phase)

  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