4FIK

Human carbonic anhydrase II H64A complexed with thioxolone hydrolysis products


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.117 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Synchrotron Radiation Provides a Plausible Explanation for the Generation of a Free Radical Adduct of Thioxolone in Mutant Carbonic Anhydrase II.

Sippel, K.H.Genis, C.Govindasamy, L.Agbandje-McKenna, M.Kiddle, J.J.Tripp, B.C.McKenna, R.

(2010) J Phys Chem Lett 1: 2898-2902

  • DOI: 10.1021/jz100954h
  • Primary Citation of Related Structures:  
    4FIK

  • PubMed Abstract: 
  • Thioxolone acts as a prodrug in the presence of carbonic anhydrase II (CA II), whereby the molecule is cleaved by thioester hydrolysis to the carbonic anhydrase inhibitor, 4-mercaptobenzene-1,3-diol (TH0). Thioxolone was soaked into the proton transfer mutant H64A of CA II in an effort to capture a reaction intermediate via X-ray crystallography ...

    Thioxolone acts as a prodrug in the presence of carbonic anhydrase II (CA II), whereby the molecule is cleaved by thioester hydrolysis to the carbonic anhydrase inhibitor, 4-mercaptobenzene-1,3-diol (TH0). Thioxolone was soaked into the proton transfer mutant H64A of CA II in an effort to capture a reaction intermediate via X-ray crystallography. Structure determination of the 1.2 Å resolution data revealed the TH0 had been modified to a 4,4'-disulfanediyldibenzene-1,3-diol, a product of crystallization conditions, and a zinc ligated 2,4-dihydroxybenzenesulfenic acid, most likely induced by radiation damage. Neither ligand was likely a result of an enzymatic mechanism.


    Related Citations: 
    • Inhibition of Carbonic Anhydrase II by Thioxolone: A Mechanistic and Structural Study
      Barrese, A.A., Genis, C., Fisher, S.Z., Orwenyo, J.N., Kumara, M.T., Dutta, S.K., Phillips, E., Kiddle, J.J., Tu, C., Silverman, D.N., Govindasamy, L., Agbandje-McKenna, M., McKenna, R., Tripp, B.C.
      (2008) Biochemistry 47: 3174

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, P.O. Box 100245, College of Medicine, University of Florida, Gainesville, Florida 32610.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 2A260Homo sapiensMutation(s): 1 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D2S
Query on D2S

Download Ideal Coordinates CCD File 
E [auth A]4,4'-disulfanediyldibenzene-1,3-diol
C12 H10 O4 S2
DCHQLQXIXWXHFP-UHFFFAOYSA-N
 Ligand Interaction
TH7
Query on TH7

Download Ideal Coordinates CCD File 
C [auth A]2,4-dihydroxybenzenesulfenic acid
C6 H6 O3 S
LJXFZIAMAZBGDO-UHFFFAOYSA-N
 Ligand Interaction
TH0
Query on TH0

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A]
4-MERCAPTOBENZENE-1,3-DIOL
C6 H6 O2 S
XFTQIEMOLHJTFV-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SO4 BindingDB:  4FIK Ki: min: 8.90e+7, max: 3.00e+8 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.117 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.37α = 90
b = 41.38β = 104.1
c = 72.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description