3SFF | pdb_00003sff

Crystal Structure of Human HDAC8 Inhibitor Complex, an Amino Acid Derived Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3SFF/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-06-13 Released: 2011-07-20 
• Deposition Author(s): Stams, T., Vash, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.221 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Human HDAC isoform selectivity achieved via exploitation of the acetate release channel with structurally unique small molecule inhibitors.

Whitehead, L., Dobler, M.R., Radetich, B., Zhu, Y., Atadja, P.W., Claiborne, T., Grob, J.E., McRiner, A., Pancost, M.R., Patnaik, A., Shao, W., Shultz, M., Tichkule, R., Tommasi, R.A., Vash, B., Wang, P., Stams, T.

(2011) Bioorg Med Chem 19: 4626-4634

• PubMed: 21723733 
• DOI: https://doi.org/10.1016/j.bmc.2011.06.030
• Primary Citation Related Structures: 
  3SFF, 3SFH


• PubMed Abstract: 
  

  Herein we report the discovery of a family of novel yet simple, amino-acid derived class I HDAC inhibitors that demonstrate isoform selectivity via access to the internal acetate release channel. Isoform selectivity criteria is discussed on the basis of X-ray crystallography and molecular modeling of these novel inhibitors bound to HDAC8, potentially revealing insights into the mechanism of enzymatic function through novel structural features revealed at the atomic level.

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Organizational Affiliation: 
• Novartis Institutes for Biomedical Research, 100 Technology Square & 250 Massachusetts Avenue, Cambridge, MA 02139, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.44 kDa 
• Atom Count: 2,928 
• Modeled Residue Count: 341 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 8	A	378	Homo sapiens	Mutation(s): 0  Gene Names: HDAC8, HDACL1, CDA07 EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY41 (Homo sapiens) Explore Q9BY41  Go to UniProtKB:  Q9BY41
PHAROS:  Q9BY41 GTEx:  ENSG00000147099

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0DI	B [auth A]	(2R)-2-amino-3-(3-chlorophenyl)-1-[4-(2,5-difluorobenzoyl)piperazin-1-yl]propan-1-one C20 H20 Cl F2 N3 O2 NASCAWUSOSJBJH-GOSISDBHSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0DI	BindingDB:  3SFF	IC50: 200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.221 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.812	α = 90
b = 53.668	β = 108.99
c = 61.338	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-20 
Deposition Author(s): Stams, T., Vash, B.

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2011-08-03
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations