7ZZU

Inhibitory Ligand binding to HDAC2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

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
KKI (Subject of Investigation/LOI)
Query on KKI

Download Ideal Coordinates CCD File 
AA [auth B],
GA [auth C],
P [auth A]
2-[4-[(2~{R},4~{S})-4-phenylpyrrolidin-2-yl]carbonylpiperazin-1-yl]pyridine-3-carbonitrile
C21 H23 N5 O
ZOCRTPMGIHWFKT-RTBURBONSA-N
NHE (Subject of Investigation/LOI)
Query on NHE

Download Ideal Coordinates CCD File 
Q [auth A]2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
PG4
Query on PG4

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

Download Ideal Coordinates CCD File 
BA [auth C]
G [auth A]
I [auth A]
J [auth A]
S [auth B]
BA [auth C],
G [auth A],
I [auth A],
J [auth A],
S [auth B],
V [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DA [auth C],
M [auth A],
X [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth C]
D [auth A]
E [auth A]
H [auth A]
K [auth A]
CA [auth C],
D [auth A],
E [auth A],
H [auth A],
K [auth A],
L [auth A],
R [auth B],
U [auth B],
W [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

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

Download Ideal Coordinates CCD File 
FA [auth C],
O [auth A],
Z [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
KKI BindingDB:  7ZZU IC50: 1800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.35α = 90
b = 98.352β = 90
c = 139.291γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
Aimlessdata 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