6BBS

Joint X-ray/neutron structure of human carbonic anhydrase II in complex with brinzolamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.276 

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    Ligand Structure Quality Assessment 


    This is version 1.1 of the entry. See complete history


    Literature

    "To Be or Not to Be" Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation.

    Kovalevsky, A.Aggarwal, M.Velazquez, H.Cuneo, M.J.Blakeley, M.P.Weiss, K.L.Smith, J.C.Fisher, S.Z.McKenna, R.

    (2018) Structure 26: 383-390.e3

    • DOI: 10.1016/j.str.2018.01.006
    • Primary Citation of Related Structures:  
      6BBS, 6BC9, 6BCC

    • PubMed Abstract: 
    • Human carbonic anhydrases (hCAs) play various roles in cells, and have been drug targets for decades. Sequence similarities of hCA isoforms necessitate designing specific inhibitors, which requires detailed structural information for hCA-inhibitor complexes ...

      Human carbonic anhydrases (hCAs) play various roles in cells, and have been drug targets for decades. Sequence similarities of hCA isoforms necessitate designing specific inhibitors, which requires detailed structural information for hCA-inhibitor complexes. We present room temperature neutron structures of hCA II in complex with three clinical drugs that provide in-depth analysis of drug binding, including protonation states of the inhibitors, hydration water structure, and direct visualization of hydrogen-bonding networks in the enzyme's active site. All sulfonamide inhibitors studied bind to the Zn metal center in the deprotonated, anionic, form. Other chemical groups of the drugs can remain neutral or be protonated when bound to hCA II. MD simulations have shown that flexible functional groups of the inhibitors may alter their conformations at room temperature and occupy different sub-sites. This study offers insights into the design of specific drugs to target cancer-related hCA isoform IX.


      Related Citations: 
      • Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules
        Adams, P.D., Mustyakimov, M., Afonine, P.V., Langan, P.
        (2009) Acta Cryst D65: 567

      Organizational Affiliation

      Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA. Electronic address: rmckenna@ufl.edu.



    Macromolecules
    Find similar proteins by:  (by identity cutoff)  |  3D Structure
    Entity ID: 1
    MoleculeChainsSequence LengthOrganismDetailsImage
    Carbonic anhydrase 2A260Homo 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
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    BZ1 (Subject of Investigation/LOI)
    Query on BZ1

    Download Ideal Coordinates CCD File 
    C [auth A](+)-4-ETHYLAMINO-3,4-DIHYDRO-2-(METHOXY)PROPYL-2H-THIENO[3,2-E]-1,2-THIAZINE-6-SULFONAMIDE-1,1-DIOXIDE
    C12 H21 N3 O5 S3
    HCRKCZRJWPKOAR-JTQLQIEISA-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
    BZ1 BindingDB:  6BBS Ki: min: 0.13, max: 45 (nM) from 6 assay(s)
    Kd: min: 0.09, max: 0.13 (nM) from 3 assay(s)
    IC50: min: 3.2, max: 45 (nM) from 2 assay(s)
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Free: 0.287 
    • R-Value Work: 0.276 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 44.755α = 90
    b = 44.011β = 104.18
    c = 75.957γ = 90
    Software Package:
    Software NamePurpose
    nCNSrefinement

    Structure Validation

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    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2018-02-28
      Type: Initial release
    • Version 1.1: 2018-03-21
      Changes: Database references