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

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

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This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1007/s00249-017-1256-0
  • Primary Citation of Related Structures:  
    5IPZ, 5JN8, 5JN9, 5JNA, 5JNC, 5KU6

  • 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 4
A, B, C, D
266Homo sapiensMutation(s): 0 
Gene Names: CA4
UniProt & NIH Common Fund Data Resources
Find proteins for P22748 (Homo sapiens)
Explore P22748 
Go to UniProtKB:  P22748
PHAROS:  P22748
GTEx:  ENSG00000167434 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22748
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EZL

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
Q [auth C],
W [auth D]
C9 H10 N2 O3 S2
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
L [auth B]
M [auth B]
R [auth C]
G [auth A],
H [auth A],
L [auth B],
M [auth B],
R [auth C],
S [auth C],
X [auth D],
Y [auth D]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
O [auth B],
T [auth C],
U [auth C]
C3 H8 O3
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
P [auth C],
V [auth D]
Query on ACT

Download Ideal Coordinates CCD File 
N [auth B],
Z [auth D]
C2 H3 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
SO4 BindingDB:  5JN9 Ki: min: 9.00e+6, max: 4.40e+7 (nM) from 2 assay(s)
ACT BindingDB:  5JN9 Ki: 5.50e+5 (nM) from 1 assay(s)
EZL BindingDB:  5JN9 Ki: min: 93, max: 840 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.784α = 90
b = 123.98β = 90
c = 151.336γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL049413
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL073813

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.2: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.3: 2022-03-23
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2023-09-27
    Changes: Data collection, Refinement description