6WBZ

Structure of Human HDAC2 in complex with an ethyl ketone inhibitor containing a spiro-bicyclic group

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Discovery of ethyl ketone-based HDACs 1, 2, and 3 selective inhibitors for HIV latency reactivation.

Yu, W., Liu, J., Yu, Y., Zhang, V., Clausen, D., Kelly, J., Wolkenberg, S., Beshore, D., Duffy, J.L., Chung, C.C., Myers, R.W., Klein, D.J., Fells, J., Holloway, K., Wu, J., Wu, G., Howell, B.J., Barnard, R.J.O., Kozlowski, J.

(2020) Bioorg Med Chem Lett 30: 127197-127197

  • DOI: https://doi.org/10.1016/j.bmcl.2020.127197
  • Primary Citation of Related Structures:  
    6WBW, 6WBZ

  • PubMed Abstract: 

    • A novel series of ethyl ketone based HDACs 1, 2, and 3 selective inhibitors have been identified with good enzymatic and cellular activity and high selectivity over HDACs 6 and 8. These inhibitors contain a spirobicyclic group in the amide region. Compound 13 stands out as a lead due to its good potency, high selectivity, and reasonable rat and dog PK ...

    A novel series of ethyl ketone based HDACs 1, 2, and 3 selective inhibitors have been identified with good enzymatic and cellular activity and high selectivity over HDACs 6 and 8. These inhibitors contain a spirobicyclic group in the amide region. Compound 13 stands out as a lead due to its good potency, high selectivity, and reasonable rat and dog PK. Compounds 33 and 34 show good potency and rat PK profiles as well.

    Organizational Affiliation: 

    Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92769
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TV7 (Subject of Investigation/LOI)
Query on TV7
Download Ideal Coordinates CCD File 
FA [auth C],
N [auth A],
V [auth B]		(1S)-N-{(1S)-7,7-dihydroxy-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]nonyl}-6-ethyl-6-azaspiro[2.5]octane-1-carboxamide
C32 H45 N5 O4
YPIRISRXAGVBOC-RSXGOPAZSA-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]
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]
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		 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 
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		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.39α = 90
b = 99.17β = 90
c = 139.6γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata 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: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-06-03
    Changes: Database references