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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
A, B
369AlcaligenesMutation(s): 0 
EC: 3.5.1.4
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6DK
Query on 6DK

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
9,9,9-tris(fluoranyl)-8,8-bis(oxidanyl)-~{N}-phenyl-nonanamide
C15 H20 F3 N O3
DOVGAPNVSPZBAT-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B],
I [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
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

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description