6XDM | pdb_00006xdm

STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN ARYL KETONE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.189 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6XDM

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Selective Class I HDAC Inhibitors Based on Aryl Ketone Zinc Binding Induce HIV-1 Protein for Clearance.

Liu, J.Kelly, J.Yu, W.Clausen, D.Yu, Y.Kim, H.Duffy, J.L.Chung, C.C.Myers, R.W.Carroll, S.Klein, D.J.Fells, J.Holloway, M.K.Wu, J.Wu, G.Howell, B.J.Barnard, R.J.O.Kozlowski, J.A.

(2020) ACS Med Chem Lett 11: 1476-1483

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00302
  • Primary Citation Related Structures: 
    6XDM

  • PubMed Abstract: 

    HIV persistence in latently infected, resting CD4 + T cells is broadly considered a barrier to eradicate HIV. Activation of the provirus using latency-reversing agents (LRAs) followed by immune-mediated clearance to purge reservoirs has been touted as a promising therapeutic approach. Histone deacetylases (HDACs) and histone acetyltransferases (HATs) control the acetylation level of lysine residues in histones to regulate the gene transcription. Several clinical HDAC inhibitors had been examined as LRAs, which induced HIV activation in vitro and in vivo. Here we report the discovery of a series of selective and potent class I HDAC inhibitors based on aryl ketones as a zinc binding group, which reversed HIV latency using a Jurkat model of HIV latency in 2C4 cells. The SAR led to the discovery of a highly selective class I HDAC inhibitor 10 with excellent potency. HDACi 10 induces the HIV gag P24 protein in patient latent CD4 + T cells.


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

Macromolecule Content 

  • Total Structure Weight: 132.74 kDa 
  • Atom Count: 10,502 
  • Modeled Residue Count: 1,101 
  • Deposited Residue Count: 1,128 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
V1D
(Subject of Investigation/LOI)

Query on V1D



Download:Ideal Coordinates CCD File
FA [auth C],
N [auth A],
V [auth B]
N-[(1S)-1-[4-(2-fluorophenyl)-1H-imidazol-2-yl]-7,7-dihydroxy-7-(1,2-oxazol-3-yl)heptyl]-1-methylazetidine-3-carboxamide
C24 H30 F N5 O4
KTQGXHKWGKIKPU-IBGZPJMESA-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]
BA [auth C]
CA [auth C]
G [auth A]
H [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
R [auth B],
S [auth B],
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
E [auth A]
F [auth A]
P [auth B]
Q [auth B]
X [auth C]
E [auth A],
F [auth A],
P [auth B],
Q [auth B],
X [auth C],
Y [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.189 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.255α = 90
b = 99.495β = 90
c = 139.85γ = 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: 2020-07-29
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references