2VCG

Crystal structure of a HDAC-like protein HDAH from Bordetella sp. with the bound inhibitor ST-17

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 

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This is version 1.4 of the entry. See complete history. 


Literature

Phenylalanine-Containing Hydroxamic Acids as Selective Inhibitors of Class Iib Histone Deacetylases (Hdacs).

Schaefer, S., Saunders, L., Eliseeva, E., Velena, A., Jung, M., Schwienhorst, A., Strasser, A., Dickmanns, A., Ficner, R., Schlimme, S., Sippl, W., Verdin, E., Jung, M.

(2008) Bioorg Med Chem 16: 2011

  • DOI: https://doi.org/10.1016/j.bmc.2007.10.092
  • Primary Citation of Related Structures:  
    2VCG

  • PubMed Abstract: 

    We synthesized biarylalanine-containing hydroxamic acids and tested them on immunoprecipitated HDAC1 and HDAC6 and show a subtype selectivity for HDAC6 that was confirmed in cells by Western blot (tubulin vs histones). We obtained an X-ray structure with a HDAC6-selective inhibitor with the bacterial deacetylase HDAH. Docking studies were carried out using HDAC1 and HDAC6 protein models. Antiproliferative activity was shown on cancer cells for selected compounds.

    • Organizational Affiliation: 

    Institute of Pharmaceutical Sciences, University of Freiburg, Albertstr. 25, 79104 Freiburg, Germany.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
A, B, C, D
375Alcaligenes sp.Mutation(s): 0 
EC: 3.5.1
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S17
Query on S17
Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
Q [auth C],
W [auth D]		methyl 4-bromo-N-[8-(hydroxyamino)-8-oxooctanoyl]-L-phenylalaninate
C18 H25 Br N2 O5
UPYGSQPRAHMDPD-HNNXBMFYSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
M [auth C],
R [auth D]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
N [auth C],
S [auth D],
T [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K
Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
J [auth B]
K [auth B]
O [auth C]
F [auth A],
G [auth A],
J [auth B],
K [auth B],
O [auth C],
P [auth C],
U [auth D],
V [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
X [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
S17 PDBBind:  2VCG IC50: 1690 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.664α = 90
b = 93.633β = 103.99
c = 121.664γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata 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: 2008-01-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description