7MOS

Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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
ZLV (Subject of Investigation/LOI)
Query on ZLV

Download Ideal Coordinates CCD File 
IA [auth C],
O [auth A],
Y [auth B]
(3S,18S,20aR)-18-(6,6-dihydroxyoctyl)-1,5,6,7,8,18,19,20a-octahydro-4H-14,17-epiminoazeto[1,2-g][1,7,10,13]benzoxatriazacycloheptadecin-20(2H)-one
C27 H40 N4 O4
UDDWOBRBECZUIE-JTHBVZDNSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
GA [auth C]
HA [auth C]
L [auth A]
M [auth A]
N [auth A]
GA [auth C],
HA [auth C],
L [auth A],
M [auth A],
N [auth A],
W [auth B],
X [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
E [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
EA [auth C]
FA [auth C]
J [auth A]
K [auth A]
U [auth B]
EA [auth C],
FA [auth C],
J [auth A],
K [auth A],
U [auth B],
V [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.447α = 90
b = 98.947β = 90
c = 139.708γ = 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: 2021-07-14
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection, Database references