6BC9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.178 

  • Method: NEUTRON DIFFRACTION

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Ligand Structure Quality Assessment 


This is version 1.2 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ETS
Query on ETS

Download Ideal Coordinates CCD File 
C [auth A](4S-TRANS)-4-(ETHYLAMINO)-5,6-DIHYDRO-6-METHYL-4H-THIENO(2,3-B)THIOPYRAN-2-SULFONAMIDE-7,7-DIOXIDE
C10 H16 N2 O4 S3
IAVUPMFITXYVAF-XPUUQOCRSA-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
ETS BindingDB:  6BC9 Ki: min: 0.2, max: 25.02 (nM) from 9 assay(s)
Kd: 0.04 (nM) from 1 assay(s)
IC50: min: 0.18, max: 43 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
  • Method: NEUTRON DIFFRACTION
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.8α = 90
b = 42.1β = 104.6
c = 72.7γ = 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
  • Version 1.2: 2018-04-25
    Changes: Data collection