5VGY

Identification of a New Zinc Binding Chemotype by Fragment Screening


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.113 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of a New Zinc Binding Chemotype by Fragment Screening.

Chrysanthopoulos, P.K.Mujumdar, P.Woods, L.A.Dolezal, O.Ren, B.Peat, T.S.Poulsen, S.A.

(2017) J. Med. Chem. 60: 7333-7349

  • DOI: 10.1021/acs.jmedchem.7b00606
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The discovery of a new zinc binding chemotype from screening a nonbiased fragment library is reported. Using the orthogonal fragment screening methods of native state mass spectrometry and surface plasmon resonance a 3-unsubstituted 2,4-oxazolidinedi ...

    The discovery of a new zinc binding chemotype from screening a nonbiased fragment library is reported. Using the orthogonal fragment screening methods of native state mass spectrometry and surface plasmon resonance a 3-unsubstituted 2,4-oxazolidinedione fragment was found to have low micromolar binding affinity to the zinc metalloenzyme carbonic anhydrase II (CA II). This affinity approached that of fragment sized primary benzenesulfonamides, the classical zinc binding group found in most CA II inhibitors. Protein X-ray crystallography established that 3-unsubstituted 2,4-oxazolidinediones bound to CA II via an interaction of the acidic ring nitrogen with the CA II active site zinc, as well as two hydrogen bonds between the oxazolidinedione ring oxygen and the CA II protein backbone. Furthermore, 3-unsubstituted 2,4-oxazolidinediones appear to be a viable starting point for the development of an alternative class of CA inhibitor, wherein the medicinal chemistry pedigree of primary sulfonamides has dominated for several decades.


    Organizational Affiliation

    Griffith University , Griffith Institute for Drug Discovery, Nathan, Brisbane, Queensland 4111, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to Gene View: CA2
Go to UniProtKB:  P00918
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9AA
Query on 9AA

Download SDF File 
Download CCD File 
A
(5S)-5-[(2,4-dimethoxyphenyl)methyl]-5-hydroxy-2-sulfanylideneimidazolidin-4-one
C12 H14 N2 O4 S
HCADMEQVRWTPEA-LBPRGKRZSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9AAKd: 65500 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.113 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.454α = 90.00
b = 41.654β = 104.29
c = 72.045γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-04-11 
  • Released Date: 2017-08-30 
  • Deposition Author(s): Peat, T.S.

Revision History 

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Database references