5LMD | pdb_00005lmd

The crystal structure of hCA II in complex with a benzoxaborole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5LMD/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2016-07-29 Released: 2016-10-19 
• Deposition Author(s): De Simone, G., Alterio, V., Esposito, D., Di Fiore, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.201 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.162 (DCC) 

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 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].
Institut des Biomolécules Max Mousseron (IBMM) UMR5247 CNRS, ENSCM, Université de Montpellier, Montpellier, France. [e-mail] and Dipartimento di Chimica e Farmacia, Università degli Studi di Sassari, Sassari, Italy.
Laboratorio di Chimica Bioinorganica, Polo Scientifico, Università degli Studi di Firenze, Sesto Fiorentino, Florence, Italy.
Dipartimento di Chimica e Farmacia, Università degli Studi di Sassari, Sassari, Italy.
Institut des Biomolécules Max Mousseron (IBMM) UMR5247 CNRS, ENSCM, Université de Montpellier, Montpellier, France. [e-mail].
Neurofarba Department, Section of Pharmaceutical and Nutriceutical Sciences, Università degli Studi di Firenze, Sesto Fiorentino, Florence, Italy.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.87 kDa 
• Atom Count: 2,340 
• Modeled Residue Count: 257 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RC4	C [auth A]	1-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-4-yl]-3-(2-methoxy-5-methyl-phenyl)urea C16 H18 B N2 O5 DMOTUOXBEBOMAL-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.201 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.162 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.427	α = 90
b = 41.493	β = 104.4
c = 72.149	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2016-10-19
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description