6VNQ

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Bishydroxamic Acid Based Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Design and Synthesis of Dihydroxamic Acids as HDAC6/8/10 Inhibitors.

Morgen, M.Steimbach, R.R.Geraldy, M.Hellweg, L.Sehr, P.Ridinger, J.Witt, O.Oehme, I.Herbst-Gervasoni, C.J.Osko, J.D.Porter, N.J.Christianson, D.W.Gunkel, N.Miller, A.K.

(2020) ChemMedChem 15: 1163-1174

  • DOI: https://doi.org/10.1002/cmdc.202000149
  • Primary Citation of Related Structures:  
    6VNQ, 6VNR

  • PubMed Abstract: 

    We report the synthesis and evaluation of a class of selective multitarget agents for the inhibition of HDAC6, HDAC8, and HDAC10. The concept for this study grew out of a structural analysis of the two selective inhibitors Tubastatin A (HDAC6/10) and PCI-34051 (HDAC8), which we recognized share the same N-benzylindole core. Hybridization of the two inhibitor structures resulted in dihydroxamic acids with benzyl-indole and -indazole core motifs. These substances exhibit potent activity against HDAC6, HDAC8, and HDAC10, while retaining selectivity over HDAC1, HDAC2, and HDAC3. The best substance inhibited the viability of the SK-N-BE(2)C neuroblastoma cell line with an IC 50 value similar to a combination treatment with Tubastatin A and PCI-34051. This compound class establishes a proof of concept for such hybrid molecules and could serve as a starting point for the further development of enhanced HDAC6/8/10 inhibitors.


  • Organizational Affiliation

    Cancer Drug Development Group, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyamine deacetylase HDAC10676Danio rerioMutation(s): 2 
Gene Names: hdac10
EC: 3.5.1.48 (PDB Primary Data), 3.5.1.62 (PDB Primary Data)
UniProt
Find proteins for F1QCV2 (Danio rerio)
Explore F1QCV2 
Go to UniProtKB:  F1QCV2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1QCV2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R5G (Subject of Investigation/LOI)
Query on R5G

Download Ideal Coordinates CCD File 
B [auth A]N-hydroxy-1-{[4-(hydroxycarbamoyl)phenyl]methyl}-1H-indole-6-carboxamide
C17 H15 N3 O4
IRJZGNPPEWBPKI-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.549α = 90
b = 80.549β = 90
c = 245.37γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM49758

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description