6RVK

Crystal structure of hCA II in complex with Urea, N-(1,3-dihydro-1-hydroxy-2,1-benzoxaborol-6-yl)-N'-(phenylmethyl)-


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Exploring benzoxaborole derivatives as carbonic anhydrase inhibitors: a structural and computational analysis reveals their conformational variability as a tool to increase enzyme selectivity.

Langella, E.Alterio, V.D'Ambrosio, K.Cadoni, R.Winum, J.Y.Supuran, C.T.Monti, S.M.De Simone, G.Di Fiore, A.

(2019) J Enzyme Inhib Med Chem 34: 1498-1505

  • DOI: 10.1080/14756366.2019.1653291
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recent studies identified the benzoxaborole moiety as a new zinc-binding group able to interact with carbonic anhydrase (CA) active site. Here, we report a structural analysis of benzoxaboroles containing urea/thiourea groups, showing that these mole ...

    Recent studies identified the benzoxaborole moiety as a new zinc-binding group able to interact with carbonic anhydrase (CA) active site. Here, we report a structural analysis of benzoxaboroles containing urea/thiourea groups, showing that these molecules are very versatile since they can bind the enzyme assuming different binding conformations and coordination geometries of the catalytic zinc ion. In addition, theoretical calculations of binding free energy were performed highlighting the key role of specific residues for protein-inhibitor recognition. Overall, these data are very useful for the development of new inhibitors with higher selectivity and efficacy for various CAs.


    Organizational Affiliation

    Neurofarba Department, Section of Pharmaceutical and Nutriceutical Sciences, Università Degli Studi di Firenze , Florence , Italy.,Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche , Naples , Italy.,Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS, ENSCM, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier , Montpellier , France.,Dipartimento di Chimica e Farmacia, Università Degli Studi di Sassari , Sassari , Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
262Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to Gene View: CA2
Go to UniProtKB:  P00918
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
R29
Query on R29

Download SDF File 
Download CCD File 
A
1-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-4-yl]-3-(phenylmethyl)urea
C15 H16 B N2 O4
OZPLHZMPGOIEJW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.350α = 90.00
b = 41.360β = 104.23
c = 72.170γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 2.0: 2019-10-30
    Type: Data collection, Derived calculations, Non-polymer description, Structure summary