6ODC

Crystal structure of HDAC8 in complex with compound 30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report



Literature

Structure-based Discovery of Novel N-(E)-N-Hydroxy-3-(2-(2-oxoimidazolidin-1-yl)phenyl)acrylamides as Potent and Selective HDAC8 inhibitors

Zheng, X.Conti, C.Caravella, J.Zablocki, M.-M.Bair, K.Barczak, N.Han, B.Lancia Jr., D.Liu, C.Martin, M.Ng, P.Y.Rudnitskaya, A.Thomason, J.J.Garcia-Dancey, R.Hardy, C.Lahdenranta, J.Leng, C.Li, P.Pardo, E.Saldahna, A.Tan, T.Toms, A.V.Yao, L.Zhang, C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase 8 ABC413Homo sapiensMutation(s): 0 
Gene Names: HDAC8HDACL1CDA07
EC: 3.5.1.98
Find proteins for Q9BY41 (Homo sapiens)
Explore Q9BY41 
Go to UniProtKB:  Q9BY41
NIH Common Fund Data Resources
PHAROS:  Q9BY41
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M7Y
Query on M7Y

Download Ideal Coordinates CCD File 
A, B, C
(2E)-3-[2-(3-cyclopentyl-5,5-dimethyl-2-oxoimidazolidin-1-yl)phenyl]-N-hydroxyprop-2-enamide
C19 H25 N3 O3
ILHJFGLWWDTUKY-VAWYXSNFSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
A, B, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.54α = 90
b = 91.161β = 94.07
c = 92.574γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2020-04-01
    Type: Initial release