6XDM

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 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

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Ligand Structure Quality Assessment 


This is version 1.0 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: 10.1021/acsmedchemlett.0c00302
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase 2A, B, C376Homo sapiensMutation(s): 0 
Gene Names: HDAC2
EC: 3.5.1.98
UniProt & NIH Common Fund Data Resources
Find proteins for Q92769 (Homo sapiens)
Explore Q92769 
Go to UniProtKB:  Q92769
PHAROS:  Q92769
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / 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
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CA [auth C] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , R [auth B] , 
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
 Ligand Interaction
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], P [auth B], Q [auth B], X [auth C], Y [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • 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

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2020-06-11 
  • Released Date: 2020-07-29 
  • Deposition Author(s): Klein, D.J., Liu, J.

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release