5JQT

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

• PDB DOI: https://doi.org/10.2210/pdb5JQT/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-05 Released: 2016-10-19 
• Deposition Author(s): Alterio, V., Esposito, D., Di Fiore, A., De Simone, G.

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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 

Starting Model: experimental

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

• PubMed: 27722534 
• 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.

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Organizational Affiliation: 

Istituto di Biostrutture e Bioimagini-CNR, Naples, Italy. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.9 kDa 
• Atom Count: 2,430 
• Modelled Residue Count: 260 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	262	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HGB	F [auth A]	4-(HYDROXYMERCURY)BENZOIC ACID C7 H6 Hg O3 WMHRYLDWLOGHSG-UHFFFAOYSA-M
6M4	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	E [auth A], G [auth A]	2,1-benzoxaborol-1(3H)-ol C7 H7 B O2 XOQABDOICLHPIS-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
6M9	BindingDB:  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 = 42.234	α = 90
b = 41.104	β = 103.92
c = 71.831	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
CrystalClear	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-19 
Deposition Author(s): Alterio, V., Esposito, D., Di Fiore, A., De Simone, G.

Revision History  

• 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
• Version 2.3: 2024-11-13
  Changes: Structure summary