6CGP | pdb_00006cgp

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with MAIP-032

• PDB DOI: https://doi.org/10.2210/pdb6CGP/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-02-20 Released: 2018-06-13 
• Deposition Author(s): Osko, J.D., Christianson, D.W.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Multicomponent Synthesis and Binding Mode of Imidazo[1,2- a]pyridine-Capped Selective HDAC6 Inhibitors.

Mackwitz, M.K.W., Hamacher, A., Osko, J.D., Held, J., Scholer, A., Christianson, D.W., Kassack, M.U., Hansen, F.K.

(2018) Org Lett 20: 3255-3258

• PubMed: 29790770 
• DOI: https://doi.org/10.1021/acs.orglett.8b01118
• Primary Citation Related Structures: 
  6CGP


• PubMed Abstract: 
  

  The multicomponent synthesis of a mini-library of histone deacetylase inhibitors with imidazo[1,2- a]pyridine-based cap groups is presented. The biological evaluation led to the discovery of the hit compound MAIP-032 as a selective HDAC6 inhibitor with promising anticancer activity. The X-ray structure of catalytic domain 2 from Danio rerio HDAC6 complexed with MAIP-032 revealed a monodentate zinc-binding mode.

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Organizational Affiliation: 
• Institut für Pharmazie , Universität Leipzig , Brüderstraße 34 , 04103 Leipzig , Germany.
Institut für Pharmazeutische und Medizinische Chemie , Heinrich-Heine-Universität Düsseldorf , Universitätsstr. 1 , 40225 Düsseldorf , Germany.
Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104-6323 , United States.
Institut für Tropenmedizin , Eberhard Karls Universität Tübingen , Wilhelmstr. 27 , 72074 Tübingen , Germany.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.8 kDa 
• Atom Count: 2,783 
• Modeled Residue Count: 357 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hdac6 protein	A	364	Danio rerio	Mutation(s): 0  Gene Names: hdac6
UniProt
Find proteins for A7YT55 (Danio rerio) Explore A7YT55  Go to UniProtKB:  A7YT55

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F1Y	E [auth A]	N-hydroxy-4-[(2-propylimidazo[1,2-a]pyridin-3-yl)amino]benzamide C17 H18 N4 O2 RDGVRQVQYOOAEK-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	B [auth A], C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.31	α = 90
b = 64.95	β = 90
c = 140.499	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): Osko, J.D., Christianson, D.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM49758

Revision History  

• Version 1.0: 2018-06-13
  Type: Initial release
  
• Version 1.1: 2018-12-26
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description