5JN9

Crystal structure for the complex of human carbonic anhydrase IV and ethoxyzolamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Intrinsic thermodynamics of high affinity inhibitor binding to recombinant human carbonic anhydrase IV.

Mickeviciute, A.Timm, D.D.Gedgaudas, M.Linkuviene, V.Chen, Z.Waheed, A.Michailoviene, V.Zubriene, A.Smirnov, A.Capkauskaite, E.Baranauskiene, L.Jachno, J.Revuckiene, J.Manakova, E.Grazulis, S.Matuliene, J.Di Cera, E.Sly, W.S.Matulis, D.

(2018) Eur. Biophys. J. 47: 271-290

  • DOI: 10.1007/s00249-017-1256-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Membrane-associated carbonic anhydrase (CA) isoform IV participates in carbon metabolism and pH homeostasis and is implicated in the development of eye diseases such as retinitis pigmentosa and glaucoma. A series of substituted benzenesulfonamides we ...

    Membrane-associated carbonic anhydrase (CA) isoform IV participates in carbon metabolism and pH homeostasis and is implicated in the development of eye diseases such as retinitis pigmentosa and glaucoma. A series of substituted benzenesulfonamides were designed and their binding affinity to CA IV was determined by fluorescent thermal shift assay and isothermal titration calorimetry (ITC). Compound [(4-chloro-2-phenylsulfanyl-5-sulfamoyl-benzoyl)amino]propyl acetate (19) bound CA IV with the K d of 1.0 nM and exhibited significant selectivity over the remaining 11 human CA isoforms. The compound could be developed as a drug targeting CA IV. Various forms of recombinant CA IV were produced in Escherichia coli and mammalian cell cultures. Comparison of their temperature stability in various buffers and salt solutions demonstrated that CA IV is most stable at slightly alkaline conditions and at elevated sodium sulfate concentrations. High-resolution X-ray crystallographic structures of ortho-Cl and meta-thiazole-substituted benzene sulfonamide in complex with CA IV revealed the position of and interactions between the ligand and the protein. Sulfonamide inhibitor binding to CA IV is linked to several reactions-the deprotonation of the sulfonamide amino group, the protonation of CA-Zn(II)-bound hydroxide at the active site of CA IV, and the compensating reactions of the buffer. The dissection of binding-linked reactions yielded the intrinsic thermodynamic parameters, characterizing the interaction between CA IV and the sulfonamides in the binding-able protonation forms, including Gibbs energy, enthalpy, and entropy, that could be used for the characterization of binding to any CA in the process of drug design.


    Related Citations: 
    • Crystal structure of the secretory form of membrane-associated human carbonic anhydrase IV at 2.8 A resolution
      Stams, T.,Nair, S.K.,Okuyama, T.,Waheed, A.,Sly, W.S.,Christianson, D.W.
      (1996) PNAS 93: 13589


    Organizational Affiliation

    Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, 10257, Vilnius, Lithuania.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 4
A, B, C, D
266Homo sapiensMutation(s): 0 
Gene Names: CA4
EC: 4.2.1.1
Find proteins for P22748 (Homo sapiens)
Go to Gene View: CA4
Go to UniProtKB:  P22748
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EZL
Query on EZL

Download SDF File 
Download CCD File 
A, B, C, D
6-ethoxy-1,3-benzothiazole-2-sulfonamide
Ethoxzolamide
C9 H10 N2 O3 S2
OUZWUKMCLIBBOG-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
B, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.784α = 90.00
b = 123.980β = 90.00
c = 151.336γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence
  • Version 1.2: 2019-02-06
    Type: Data collection, Database references