5JQT

Crystal structure of human carbonic anhydrase II in complex with Benzoxaborole at pH 7.4

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.123 

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This is version 2.2 of the entry. See complete history. 


Literature

Benzoxaborole as a new chemotype for carbonic anhydrase inhibition.

Alterio, V., Cadoni, R., Esposito, D., Vullo, D., Fiore, A.D., Monti, S.M., Caporale, A., Ruvo, M., Sechi, M., Dumy, P., Supuran, C.T., Simone, G., Winum, J.Y.

(2016) Chem Commun (Camb) 52: 11983-11986

  • DOI: https://doi.org/10.1039/c6cc06399c
  • Primary Citation of Related Structures:  
    5JQ0, 5JQT, 5LMD

  • PubMed Abstract: 

    In this paper we report the synthesis of a series of benzoxaborole derivatives, their inhibition properties against some carbonic anhydrases (CAs), recognized as important drug targets, and the characterization of the binding mode of these molecules to the CA active site. Our data provide the first experimental evidence that benzoxaboroles can be efficiently used as CA inhibitors.

    • Organizational Affiliation: 

    Istituto di Biostrutture e Bioimagini-CNR, Naples, Italy. gdesimon@unina.it.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2262Homo 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
GTEx:  ENSG00000104267 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HGB
Query on HGB
Download Ideal Coordinates CCD File 
F [auth A]4-(HYDROXYMERCURY)BENZOIC ACID
C7 H6 Hg O3
WMHRYLDWLOGHSG-UHFFFAOYSA-M
6M4
Query on 6M4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth A],
I [auth A],
J [auth A]		1,1-dihydroxy-1,3-dihydro-2,1-benzoxaborol-1-ium
C7 H8 B O3
LFYLOXDIRWAWMG-UHFFFAOYSA-N
6M9
Query on 6M9
Download Ideal Coordinates CCD File 
E [auth A],
G [auth A]		2,1-benzoxaborol-1(3H)-ol
C7 H7 B O2
XOQABDOICLHPIS-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6M9 BindingDB:  5JQT Ki: 8180 (nM) from 1 assay(s)
Binding MOAD:  5JQT Ki: 8180 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.123 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.234α = 90
b = 41.104β = 103.92
c = 71.831γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata reduction
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 2.0: 2019-10-30
    Changes: Data collection, Derived calculations, Non-polymer description
  • Version 2.1: 2019-11-20
    Changes: Derived calculations
  • Version 2.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description