7ZZW

Ligand binding to HDAC2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Fragment-Based Discovery of a Novel, Brain Penetrant, Orally Active HDAC2 Inhibitor.

Tamanini, E.Miyamura, S.Buck, I.M.Cons, B.D.Dawson, L.East, C.Futamura, T.Goto, S.Griffiths-Jones, C.Hashimoto, T.Heightman, T.D.Ishikawa, S.Ito, H.Kaneko, Y.Kawato, T.Kondo, K.Kurihara, N.McCarthy, J.M.Mori, Y.Nagase, T.Nakaishi, Y.Reeks, J.Sato, A.Schopf, P.Tai, K.Tamai, T.Tisi, D.Woolford, A.J.

(2022) ACS Med Chem Lett 13: 1591-1597

  • DOI: https://doi.org/10.1021/acsmedchemlett.2c00272
  • Primary Citation of Related Structures:  
    7ZZO, 7ZZP, 7ZZR, 7ZZS, 7ZZT, 7ZZU, 7ZZW, 8A0B

  • PubMed Abstract: 

    Fragment-based ligand discovery was successfully applied to histone deacetylase HDAC2. In addition to the anticipated hydroxamic acid- and benzamide-based fragment screening hits, a low affinity (∼1 mM) α-amino-amide zinc binding fragment was identified, as well as fragments binding to other regions of the catalytic site. This alternative zinc-binding fragment was further optimized, guided by the structural information from protein-ligand complex X-ray structures, into a sub-μM, brain penetrant, HDAC2 inhibitor ( 17 ) capable of modulating histone acetylation levels in vivo .


  • Organizational Affiliation

    Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 2
A, B, C
498Homo sapiensMutation(s): 0 
Gene Names: HDAC2
EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (PDB Primary Data)
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 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KKW (Subject of Investigation/LOI)
Query on KKW

Download Ideal Coordinates CCD File 
EA [auth C],
L [auth A],
W [auth B]
[(2~{R},4~{S})-4-(3-chlorophenyl)pyrrolidin-2-yl]-(4-thieno[2,3-c]pyridin-7-ylpiperazin-1-yl)methanone
C22 H23 Cl N4 O S
YMNUWCFQVRYQGA-IEBWSBKVSA-N
KZF
Query on KZF

Download Ideal Coordinates CCD File 
M [auth A]2-(cyclohexylazaniumyl)ethanesulfonate
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
F [auth A],
X [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
H [auth A]
O [auth B]
P [auth B]
D [auth A],
E [auth A],
H [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
Y [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth C],
I [auth A],
T [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C],
G [auth A],
N [auth B],
S [auth B],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth C],
J [auth A],
U [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
DA [auth C],
K [auth A],
V [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
KKW BindingDB:  7ZZW IC50: 500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.149α = 90
b = 97.934β = 90
c = 139.538γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
XDSdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-11-02
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection