7MOY

Structure of HDAC2 in complex with an inhibitor (compound 19)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.208 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ZLMClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Discovery of macrocyclic HDACs 1, 2, and 3 selective inhibitors for HIV latency reactivation.

Yu, W.Fells, J.Clausen, D.Liu, J.Klein, D.J.Christine Chung, C.Myers, R.W.Wu, J.Wu, G.Howell, B.J.Barnard, R.J.O.Kozlowski, J.

(2021) Bioorg Med Chem Lett 47: 128168-128168

  • DOI: https://doi.org/10.1016/j.bmcl.2021.128168
  • Primary Citation of Related Structures:  
    7MOS, 7MOT, 7MOX, 7MOY, 7MOZ

  • PubMed Abstract: 

    A series of unique macrocyclic HDACs 1, 2, and 3 selective inhibitors were identified with good enzymatic activity and high selectivity over HDACs 6 and 8. These macrocyclic HDAC inhibitors used an ethyl ketone as the zinc-binding group. Compounds 25 and 26 stood out as leads due to their low double-digit nM EC 50 s in the 2C4 cell-based HIV latency reactivation assay. The PK profiles of these macrocyclic HDAC inhibitors still needed improvement.


  • Organizational Affiliation

    Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA. Electronic address: wenshengyu@msn.com.


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
ZLM (Subject of Investigation/LOI)
Query on ZLM

Download Ideal Coordinates CCD File 
FA [auth C],
N [auth A],
V [auth B]
(1S)-6-ethyl-N-{(1S)-1-[5-(2-ethyl-1-oxo-1,2-dihydroisoquinolin-6-yl)-1H-imidazol-2-yl]-7,7-dihydroxynonyl}-6-azaspiro[2.5]octane-1-carboxamide
C33 H47 N5 O4
UGJJVROKAWKMLZ-SXOMAYOGSA-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]
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]
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]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.398α = 90
b = 99.141β = 90
c = 139.794γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ZLMClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2021-11-24
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection