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

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This is version 1.1 of the entry. See complete history


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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 8
A, B, C
413Homo sapiensMutation(s): 0 
Gene Names: HDAC8HDACL1CDA07
EC: 3.5.1.98
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY41 (Homo sapiens)
Explore Q9BY41 
Go to UniProtKB:  Q9BY41
PHAROS:  Q9BY41
GTEx:  ENSG00000147099 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BY41
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M7Y (Subject of Investigation/LOI)
Query on M7Y

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B],
S [auth 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
ZN
Query on ZN

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

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

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
L [auth B]
M [auth B]
Q [auth C]
E [auth A],
F [auth A],
L [auth B],
M [auth B],
Q [auth C],
R [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
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

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description