4WW6

Crystal structure of human carbonic anhydrase isozyme II with 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.131 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Intrinsic thermodynamics of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamide binding to carbonic anhydrases by isothermal titration calorimetry.

Zubriene, A.Smirnoviene, J.Smirnov, A.Morkunaite, V.Michailoviene, V.Jachno, J.Juozapaitiene, V.Norvaisas, P.Manakova, E.Grazulis, S.Matulis, D.

(2015) Biophys Chem 205: 51-65

  • DOI: 10.1016/j.bpc.2015.05.009
  • Primary Citation of Related Structures:  
    4WR7, 4WUP, 4WUQ, 4WW6, 4WW8

  • PubMed Abstract: 
  • Para substituted tetrafluorobenzenesulfonamides bind to carbonic anhydrases (CAs) extremely tightly and exhibit some of the strongest known protein-small ligand interactions, reaching an intrinsic affinity of 2 pM as determined by displacement isothe ...

    Para substituted tetrafluorobenzenesulfonamides bind to carbonic anhydrases (CAs) extremely tightly and exhibit some of the strongest known protein-small ligand interactions, reaching an intrinsic affinity of 2 pM as determined by displacement isothermal titration calorimetry (ITC). The enthalpy and entropy of binding to five CA isoforms were measured by ITC in two buffers of different protonation enthalpies. The pKa values of compound sulfonamide groups were measured potentiometrically and spectrophotometrically, and enthalpies of protonation were measured by ITC in order to evaluate the proton linkage contributions to the observed binding thermodynamics. Intrinsic means the affinity of a sulfonamide anion for the Zn bound water form of CAs. Fluorination of the benzene ring significantly enhanced the observed affinities as it increased the fraction of deprotonated ligand while having little impact on intrinsic affinities. Intrinsic enthalpy contributions to the binding affinity were dominant over entropy and were more exothermic for CA I than for other CA isoforms. Thermodynamic measurements together with the X-ray crystallographic structures of protein-ligand complexes enabled analysis of structure-activity relationships in this enzyme ligand system.


    Organizational Affiliation

    Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 2A260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
NIH Common Fund Data Resources
PHAROS  P00918
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3TV
Query on 3TV

Download CCD File 
A
2,3,5,6-tetrafluoro-4-(propylsulfanyl)benzenesulfonamide
C9 H9 F4 N O2 S2
LKPIFWBRFVJTMY-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
BCN
Query on BCN

Download CCD File 
A
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
 Ligand Interaction
MLA
Query on MLA

Download CCD File 
A
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3TVKd:  2   nM  BindingDB
3TVKd:  0.06199999898672104   nM  Binding MOAD
3TVKd:  0.9100000262260437   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.131 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.214α = 90
b = 41.026β = 104.29
c = 71.774γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
SCALAdata scaling
Cootmodel building
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Data collection