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BioAssay: AID 269135

Inhibition of Escherichia coli KPR

Mapping interactions at protein-ligand binding sites is an important aspect of understanding many biological reactions and a key part of drug design. In this paper, we have used a fragment-based approach to probe "hot spots" at the cofactor-binding site of a model dehydrogenase, Escherichia coli ketopantoate reductase. Our strategy involved the breaking down of NADPH (Kd = 300 nM) into more ..
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 Tested Compounds
 Tested Compounds
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Unspecified(7)
 
 
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 Tested Substances
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Unspecified(7)
 
 
 Related BioAssays
 Related BioAssays
AID: 269135
Data Source: ChEMBL (382750)
BioAssay Type: Confirmatory, Concentration-Response Relationship Observed
Depositor Category: Literature, Extracted
BioAssay Version:
Deposit Date: 2010-05-25
Modify Date: 2014-08-25

Data Table ( Complete ):           View All Data
Tested Compounds:
Description:
Title: Probing hot spots at protein-ligand binding sites: a fragment-based approach using biophysical methods.

Abstract: Mapping interactions at protein-ligand binding sites is an important aspect of understanding many biological reactions and a key part of drug design. In this paper, we have used a fragment-based approach to probe "hot spots" at the cofactor-binding site of a model dehydrogenase, Escherichia coli ketopantoate reductase. Our strategy involved the breaking down of NADPH (Kd = 300 nM) into smaller fragments and the biophysical characterization of their binding using WaterLOGSY NMR spectroscopy, isothermal titration calorimetry (ITC), and inhibition studies. The weak binding affinities of fragments were measured by direct ITC titrations under low c value conditions. The 2'-phosphate and the reduced nicotinamide groups were found to contribute a large part of the binding energy. A combination of ITC and site-directed mutagenesis enabled us to locate the fragments at separate hot spots on opposite ends of the cofactor-binding site. This study has identified structural determinants for cofactor recognition that represent a blueprint for future inhibitor design.
(PMID: 16884311)
Comment
Putative Target:
ChEMBL Target ID: 100777
Target Type: SINGLE PROTEIN
Pref Name: Ketopantoate reductase
Synonyms: 2-dehydropantoate 2-reductase;Ketopantoate reductase;KPA reductase;KPR;
Gene Name: apbA;JW0415;panE;
Protein Accession: P0A9J4;
Protein GI: 71159619;
Organism: Escherichia coli K-12
Tax ID: 83333
Target Classification: enzyme
Confidence: Homologous single protein target assigned
Relationship Type: Homologous protein target assigned
Categorized Comment - additional comments and annotations
From BioAssay Depositor:
Assay Type: Binding
Assay Data Source: Scientific Literature
Result Definitions
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TIDNameDescriptionHistogramTypeUnit
OutcomeThe BioAssay activity outcomeOutcome
1Ki*Ki PubChem standard valueFloatμM
3BEIBinding Efficiency Index(nM)Float
2SEISurface Efficiency Index(nM)Float
4LELigand EfficiencyFloat
5LLELipophilic Ligand EfficiencyFloat
6Ki activity commentKi activity commentString
7Ki standard flagKi standard flagInteger
8Ki qualifierKi qualifierString
9Ki published valueKi published valueFloatmM
10Ki standard valueKi standard valueFloatnM
11Ki data validityKi data validityString
12Km activity commentKm activity commentString
13Km standard flagKm standard flagInteger
14Km qualifierKm qualifierString
15Km published valueKm published valueFloatmM
16Km standard valueKm standard valueFloatnM
17Km data validityKm data validityString

* Activity Concentration.

Data Table (Concise)
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