2V5X

Crystal structure of HDAC8-inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Substrate Binding to Histone Deacetylases as Revealed by Crystal Structure of Hdac8-Substrate Complex

Vannini, A.Volpari, C.Gallinari, P.Jones, P.Mattu, M.Carfi, A.Defrancesco, R.Steinkuhler, C.Di Marco, S.

(2007) Embo Rep. 8: 879

  • DOI: 10.1038/sj.embor.7401047
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Histone deacetylases (HDACs)-an enzyme family that deacetylates histones and non-histone proteins-are implicated in human diseases such as cancer, and the first-generation of HDAC inhibitors are now in clinical trials. Here, we report the 2.0 A resol ...

    Histone deacetylases (HDACs)-an enzyme family that deacetylates histones and non-histone proteins-are implicated in human diseases such as cancer, and the first-generation of HDAC inhibitors are now in clinical trials. Here, we report the 2.0 A resolution crystal structure of a catalytically inactive HDAC8 active-site mutant, Tyr306Phe, bound to an acetylated peptidic substrate. The structure clarifies the role of active-site residues in the deacetylation reaction and substrate recognition. Notably, the structure shows the unexpected role of a conserved residue at the active-site rim, Asp 101, in positioning the substrate by directly interacting with the peptidic backbone and imposing a constrained cis-conformation. A similar interaction is observed in a new hydroxamate inhibitor-HDAC8 structure that we also solved. The crucial role of Asp 101 in substrate and inhibitor recognition was confirmed by activity and binding assays of wild-type HDAC8 and Asp101Ala, Tyr306Phe and Asp101Ala/Tyr306Phe mutants.


    Organizational Affiliation

    Istituto di Ricerche di Biologia Molecolare P. Angeletti, Via Pontina Km 30.600, 00040 Pomezia, Rome, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HISTONE DEACETYLASE 8
A, B
388Homo sapiensMutation(s): 1 
Gene Names: HDAC8 (HDACL1)
EC: 3.5.1.98
Find proteins for Q9BY41 (Homo sapiens)
Go to Gene View: HDAC8
Go to UniProtKB:  Q9BY41
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
V5X
Query on V5X

Download SDF File 
Download CCD File 
A, B
(2R)-N~8~-HYDROXY-2-{[(5-METHOXY-2-METHYL-1H-INDOL-3-YL)ACETYL]AMINO}-N~1~-[2-(2-PHENYL-1H-INDOL-3-YL)ETHYL]OCTANEDIAMIDE
C36 H41 N5 O5
VBWCMILVHANAGG-JGCGQSQUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
V5XIC50: 100 nM BINDINGMOAD
V5XKd: 220 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.298α = 90.00
b = 98.694β = 90.00
c = 110.474γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-04
    Type: Initial release
  • Version 1.1: 2012-09-12
    Type: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance