6CW8

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with RTS-V5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of the First-in-Class Dual Histone Deacetylase-Proteasome Inhibitor.

Bhatia, S.Krieger, V.Groll, M.Osko, J.D.Ahlert, H.Borkhardt, A.Kurz, T.Christianson, D.W.Hauer, J.Hansen, F.K.

(2018) J Med Chem 61: 10299-10309

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01487
  • Primary Citation of Related Structures:  
    6CW8, 6H39

  • PubMed Abstract: 

    Dual- or multitarget drugs have emerged as a promising alternative to combination therapies. Proteasome inhibitors (PIs) possess synergistic activity with histone deacetylase (HDAC) inhibitors due to the simultaneous blockage of the ubiquitin degradation and aggresome pathways. Here, we present the design, synthesis, binding modes, and anticancer properties of RTS-V5 as the first-in-class dual HDAC-proteasome ligand. The inhibition of both targets was confirmed by biochemical and cellular assays as well as X-ray crystal structures of the 20S proteasome and HDAC6 complexed with RTS-V5. Cytotoxicity assays with leukemia and multiple myeloma cell lines as well as therapy refractory primary patient-derived leukemia cells demonstrated that RTS-V5 possesses potent and selective anticancer activity. Our results will thus guide the structure-based optimization of dual HDAC-proteasome inhibitors for the treatment of hematological malignancies.


  • Organizational Affiliation

    Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty , Heinrich Heine University Düsseldorf , Moorenstrasse 5 , 40225 Düsseldorf , Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hdac6 protein
A, B
364Danio rerioMutation(s): 0 
Gene Names: hdac6
UniProt
Find proteins for F8W4B7 (Danio rerio)
Explore F8W4B7 
Go to UniProtKB:  F8W4B7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8W4B7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FGY
Query on FGY

Download Ideal Coordinates CCD File 
F [auth A],
O [auth B]
N-(2,2-dimethylpropyl)-N~2~-[4-(hydroxycarbamoyl)benzene-1-carbonyl]-L-asparaginyl-N-benzyl-L-alaninamide
C27 H35 N5 O6
CMINWSPSBRREEO-UWJYYQICSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
L [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
M [auth B],
N [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.31α = 90
b = 128.43β = 90
c = 260.49γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2018-11-21
    Type: Initial release
  • Version 1.1: 2019-01-16
    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