7KBG

Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 20)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 


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Literature

Discovery of Highly Selective and Potent HDAC3 Inhibitors Based on a 2-Substituted Benzamide Zinc Binding Group.

Liu, J., Yu, Y., Kelly, J., Sha, D., Alhassan, A.B., Yu, W., Maletic, M.M., Duffy, J.L., Klein, D.J., Holloway, M.K., Carroll, S., Howell, B.J., Barnard, R.J.O., Wolkenberg, S., Kozlowski, J.A.

(2020) ACS Med Chem Lett 11: 2476-2483

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00462
  • Primary Citation of Related Structures:  
    7KBG, 7KBH

  • PubMed Abstract: 

    • The selectivity of histone deacetylase inhibitors (HDACis) is greatly impacted by the zinc binding groups. In an effort to search for novel zinc binding groups, we applied a parallel medicinal chemistry (PMC) strategy to quickly synthesize substituted benzamide libraries ...

    The selectivity of histone deacetylase inhibitors (HDACis) is greatly impacted by the zinc binding groups. In an effort to search for novel zinc binding groups, we applied a parallel medicinal chemistry (PMC) strategy to quickly synthesize substituted benzamide libraries. We discovered a series containing 2-substituted benzamides as the zinc binding group which afforded highly selective and potent HDAC3 inhibitors, exemplified by compound 16 with a 2-methylthiobenzamide. Compound 16 inhibited HDAC3 with an IC 50 of 30 nM and with unprecedented selectivity of >300-fold over all other HDAC isoforms. Interestingly, a subtle change of the 2-methylthio to a 2-hydroxy benzamide in 20 retains HDAC3 potency but loses all selectivity over HDAC 1 and 2. This significant difference in selectivity was rationalized by X-ray crystal structures of HDACis 16 and 20 bound to HDAC2, revealing different binding modes to the catalytic zinc ion. This series of HDAC3 selective inhibitors served as tool compounds for investigating the minimal set of HDAC isoforms that must be inhibited for the HIV latency activation in a Jurkat 2C4 cell model and potentially as leads for selective HDAC3 inhibitors for other indications.

    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase 2A, B, C376Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92769
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WBA (Subject of Investigation/LOI)
Query on WBA
Download Ideal Coordinates CCD File 
IA [auth C],
N [auth A],
W [auth B]		N-{(1S)-5-[(2-fluoro-6-hydroxybenzene-1-carbonyl)amino]-1-[5-(naphthalen-2-yl)-1H-imidazol-2-yl]pentyl}-1,3-thiazole-5-carboxamide
C29 H26 F N5 O3 S
BBLOAIWXSMVTHJ-QFIPXVFZSA-N		 Ligand Interaction
WBD
Query on WBD
Download Ideal Coordinates CCD File 
HA [auth C]2,5-dichloro-1H-benzimidazole
C7 H4 Cl2 N2
LLIARSREYVCQHL-UHFFFAOYSA-N		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
FA [auth C],
GA [auth C],
K [auth A],
L [auth A],
M [auth A],
FA [auth C],
GA [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 
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
G [auth A],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
R [auth B],
S [auth B],
V [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
X [auth C]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
D [auth A],
O [auth B],
Y [auth C]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
AA [auth C],
E [auth A],
F [auth A],
P [auth B],
Q [auth B],
AA [auth C],
E [auth A],
F [auth A],
P [auth B],
Q [auth B],
Z [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
WBA Binding MOAD:  7KBG IC50: 29 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.26α = 90
b = 99.27β = 90
c = 139.02γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release