5G17

Bordetella Alcaligenes HDAH (T101A) bound to 9,9,9-trifluoro-8,8- dihydroxy-N-phenylnonanamide.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 

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This is version 1.2 of the entry. See complete history. 


Literature

The thermodynamic signature of ligand binding to histone deacetylase-like amidohydrolases is most sensitive to the flexibility in the L2-loop lining the active site pocket.

Meyners, C., Kramer, A., Yildiz, O., Meyer-Almes, F.J.

(2017) Biochim Biophys Acta 1861: 1855-1863

  • DOI: 10.1016/j.bbagen.2017.04.001
  • Primary Citation of Related Structures:  
    5G17, 5G1A, 5G1B

  • PubMed Abstract: 

    • The analysis of the thermodynamic driving forces of ligand-protein binding has been suggested to be a key component for the selection and optimization of active compounds into drug candidates. The binding enthalpy as deduced from isothermal titration calorimetry (ITC) is usually interpreted assuming single-step binding of a ligand to one conformation of the target protein ...

    The analysis of the thermodynamic driving forces of ligand-protein binding has been suggested to be a key component for the selection and optimization of active compounds into drug candidates. The binding enthalpy as deduced from isothermal titration calorimetry (ITC) is usually interpreted assuming single-step binding of a ligand to one conformation of the target protein. Although successful in many cases, these assumptions are oversimplified approximations of the reality with flexible proteins and complicated binding mechanism in many if not most cases. The relationship between protein flexibility and thermodynamic signature of ligand binding is largely understudied.

    Organizational Affiliation: 

    Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany. Electronic address: franz-josef.meyer-almes@h-da.de.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE DEACETYLASE-LIKE AMIDOHYDROLASEA, B369AlcaligenesMutation(s): 0 
EC: 3.5.1.4 (PDB Primary Data), 3.5.1 (UniProt)
UniProt
Find proteins for Q70I53 (Alcaligenes sp. (strain DSM 11172))
Explore Q70I53 
Go to UniProtKB:  Q70I53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70I53
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
6DK Binding MOAD:  5G17 Kd: 200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.27α = 90
b = 101.27β = 90
c = 175.22γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-04-19
    Changes: Database references
  • Version 1.2: 2017-07-05
    Changes: Database references