7MOT

Structure of HDAC2 in complex with an inhibitor (compound 9)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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
V1P (Subject of Investigation/LOI)
Query on V1P

Download Ideal Coordinates CCD File 
FA [auth C],
N [auth A],
V [auth B]
5-{(1S)-7,7-dihydroxy-1-[(1-methylazetidine-3-carbonyl)amino]nonyl}-2-phenyl-1H-imidazole-4-carboxamide
C24 H35 N5 O4
MYVMGGDKZVVQFO-SFHVURJKSA-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: 1.54 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.417α = 90
b = 99.064β = 90
c = 139.622γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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