6R6F

Crystal structure of human carbonic anhydrase isozyme II with 4-chloro-2-cyclohexylsulfanyl-N-(2-hydroxyethyl)-5-sulfamoyl-benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Halogenated and di-substituted benzenesulfonamides as selective inhibitors of carbonic anhydrase isoforms.

Zaksauskas, A.Capkauskaite, E.Jezepcikas, L.Linkuviene, V.Paketuryte, V.Smirnov, A.Leitans, J.Kazaks, A.Dvinskis, E.Manakova, E.Grazulis, S.Tars, K.Matulis, D.

(2020) Eur J Med Chem 185: 111825-111825

  • DOI: https://doi.org/10.1016/j.ejmech.2019.111825
  • Primary Citation of Related Structures:  
    6QN0, 6QN2, 6QN5, 6QN6, 6QNL, 6QUT, 6R6F, 6R6J, 6R6Y, 6R71

  • PubMed Abstract: 

    By applying an approach of a "ring with two tails", a series of novel inhibitors possessing high-affinity and significant selectivity towards selected carbonic anhydrase (CA) isoforms has been designed. The "ring" consists of 2-chloro/bromo-benzenesulfonamide, where the sulfonamide group is as an anchor coordinating the Zn(II) in the active site of CAs, and halogen atom orients the ring affecting the affinity and selectivity. First "tail" is a substituent containing carbonyl, carboxyl, hydroxyl, ether groups or hydrophilic amide linkage. The second "tail" contains aryl- or alkyl-substituents attached through a sulfanyl or sulfonyl group. Both "tails" are connected to the benzene ring and play a crucial role in selectivity. Varying the substituents, we designed compounds selective for CA VII, CA IX, CA XII, or CA XIV. Since due to binding-linked protonation reactions the binding-ready fractions of the compound and protein are much lower than one, the "intrinsic" affinities were calculated that should be used to study correlations between crystal structures and the thermodynamics of binding for rational drug design. The "intrinsic" affinities together with the intrinsic enthalpies and entropies of binding together with co-crystal structures were used demonstrate structural factors determining major contributions for compound affinity and selectivity.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
PHAROS:  P00918
GTEx:  ENSG00000104267 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EA3
Query on EA3

Download Ideal Coordinates CCD File 
C [auth A]4-chloranyl-2-cyclohexylsulfanyl-~{N}-(2-hydroxyethyl)-5-sulfamoyl-benzamide
C15 H21 Cl N2 O4 S2
PSEDAEWMXCWYRT-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
D [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.149 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.308α = 90
b = 41.749β = 104.19
c = 72.323γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Database references
  • Version 1.2: 2020-04-01
    Changes: Database references
  • Version 1.3: 2021-10-06
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2024-01-24
    Changes: Data collection, Refinement description