4FIK

Human carbonic anhydrase II H64A complexed with thioxolone hydrolysis products


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.116 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  3IQK

  • 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 transf ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
260Homo sapiensGene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to Gene View: CA2
Go to UniProtKB:  P00918
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TH0
Query on TH0

Download SDF File 
Download CCD File 
A
4-MERCAPTOBENZENE-1,3-DIOL
C6 H6 O2 S
XFTQIEMOLHJTFV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
TH7
Query on TH7

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Download CCD File 
A
2,4-dihydroxybenzenesulfenic acid
4-HYDROXYSULFANYLBENZENE-1,3-DIOL
C6 H6 O3 S
LJXFZIAMAZBGDO-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
D2S
Query on D2S

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Download CCD File 
A
4,4'-disulfanediyldibenzene-1,3-diol
4-(2,4-dihydroxyphenyl)disulfanylbenzene-1,3-diol
C12 H10 O4 S2
DCHQLQXIXWXHFP-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SO4Ki: 89000000 - >300000000 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.116 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.370α = 90.00
b = 41.380β = 104.10
c = 72.060γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description