7JS8

STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN ETHYL KETONE INHIBITOR CONTAINING A SPIRO-BICYCLIC GROUP (COMPOUND 22)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of Ethyl Ketone-Based Highly Selective HDACs 1, 2, 3 Inhibitors for HIV Latency Reactivation with Minimum Cellular Potency Serum Shift and Reduced hERG Activity.

Yu, W.Liu, J.Clausen, D.Yu, Y.Duffy, J.L.Wang, M.Xu, S.Deng, L.Suzuki, T.Chung, C.C.Myers, R.W.Klein, D.J.Fells, J.I.Holloway, M.K.Wu, J.Wu, G.Howell, B.J.Barnard, R.J.O.Kozlowski, J.

(2021) J Med Chem 64: 4709-4729

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02150
  • Primary Citation of Related Structures:  
    7JS8

  • PubMed Abstract: 

    We describe the discovery of histone deacetylase (HDACs) 1, 2, and 3 inhibitors with ethyl ketone as the zinc-binding group. These HDACs 1, 2, and 3 inhibitors have good enzymatic and cellular activity. Their serum shift in cellular potency has been minimized, and selectivity against hERG has been improved. They are also highly selective over HDACs 6 and 8. These inhibitors contain a variety of substituted heterocycles on the imidazole or oxazole scaffold. Compounds 31 and 48 stand out due to their good potency, high selectivity over HDACs 6 and 8, reduced hERG activity, optimized serum shift in cellular potency, and good rat and dog PK profiles.


  • Organizational Affiliation

    Merck & Co. Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 2
A, B, C
376Homo sapiensMutation(s): 0 
Gene Names: HDAC2
EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92769 (Homo sapiens)
Explore Q92769 
Go to UniProtKB:  Q92769
PHAROS:  Q92769
GTEx:  ENSG00000196591 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92769
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VJV (Subject of Investigation/LOI)
Query on VJV

Download Ideal Coordinates CCD File 
FA [auth C],
N [auth A],
V [auth B]
(1S)-N-{(1S)-7,7-dihydroxy-1-[4-(2-methylquinolin-6-yl)-1H-imidazol-2-yl]nonyl}-6-methyl-6-azaspiro[2.5]octane-1-carboxamide
C31 H43 N5 O3
TUQSZAQBKOXAIB-RSXGOPAZSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
DA [auth C]
EA [auth C]
K [auth A]
L [auth A]
M [auth A]
DA [auth C],
EA [auth C],
K [auth A],
L [auth A],
M [auth A],
T [auth B],
U [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
AA [auth C],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
P [auth B],
Q [auth B],
X [auth C],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
O [auth B],
W [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
I [auth A]
J [auth A]
R [auth B]
BA [auth C],
CA [auth C],
I [auth A],
J [auth A],
R [auth B],
S [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.43α = 90
b = 99.16β = 90
c = 139.65γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection