Crystal structure of S39D HDAC8 in complex with a largazole analogue.

Experimental Data Snapshot

  • Resolution: 2.39 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

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This is version 1.2 of the entry. See complete history


Variable Active Site Loop Conformations Accommodate the Binding of Macrocyclic Largazole Analogues to HDAC8.

Decroos, C.Clausen, D.J.Haines, B.E.Wiest, O.Williams, R.M.Christianson, D.W.

(2015) Biochemistry 54: 2126-2135

  • DOI: https://doi.org/10.1021/acs.biochem.5b00010
  • Primary Citation of Related Structures:  
    4RN0, 4RN1, 4RN2

  • PubMed Abstract: 

    The macrocyclic depsipeptide Largazole is a potent inhibitor of metal-dependent histone deacetylases (HDACs), some of which are drug targets for cancer chemotherapy. Indeed, Largazole partially resembles Romidepsin (FK228), a macrocyclic depsipeptide already approved for clinical use. Each inhibitor contains a pendant side chain thiol that coordinates to the active site Zn(2+) ion, as observed in the X-ray crystal structure of the HDAC8-Largazole complex [Cole, K. E., Dowling, D. P., Boone, M. A., Phillips, A. J., and Christianson, D. W. (2011) J. Am. Chem. Soc. 133, 12474]. Here, we report the X-ray crystal structures of HDAC8 complexed with three synthetic analogues of Largazole in which the depsipeptide ester is replaced with a rigid amide linkage. In two of these analogues, a six-membered pyridine ring is also substituted (with two different orientations) for the five-membered thiazole ring in the macrocycle skeleton. The side chain thiol group of each analogue coordinates to the active site Zn(2+) ion with nearly ideal geometry, thereby preserving the hallmark structural feature of inhibition by Largazole. Surprisingly, in comparison with the binding of Largazole, these analogues trigger alternative conformational changes in loops L1 and L2 flanking the active site. However, despite these structural differences, inhibitory potency is generally comparable to, or just moderately less than, the inhibitory potency of Largazole. Thus, this study reveals important new structure-affinity relationships for the binding of macrocyclic inhibitors to HDAC8.

  • Organizational Affiliation

    †Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 8
A, B
389Homo sapiensMutation(s): 1 
Gene Names: HDAC8HDACL1CDA07
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY41 (Homo sapiens)
Explore Q9BY41 
Go to UniProtKB:  Q9BY41
GTEx:  ENSG00000147099 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BY41
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on L7G

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
C23 H31 N5 O3 S2
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
Query on K

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B],
I [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
L7G BindingDB:  4RN2 IC50: 1491 (nM) from 1 assay(s)
Binding MOAD:  4RN2 IC50: 1500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.39 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.764α = 90
b = 84.712β = 100.47
c = 94.139γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-04-22
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description