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

  • Resolution: 1.70 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.179 

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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: https://doi.org/10.1080/14756366.2019.1653291
  • Primary Citation of Related Structures:  
    6RVF, 6RVK, 6RVL, 6RW1

  • 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 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

    Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche , Naples , Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2262Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: (PDB Primary Data), (UniProt)
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
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KL5 (Subject of Investigation/LOI)
Query on KL5

Download Ideal Coordinates CCD File 
C [auth A]1-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-trien-4-yl]-3-(phenylmethyl)thiourea
C15 H16 B N2 O3 S
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Binding Affinity Annotations 
IDSourceBinding Affinity
KL5 Binding MOAD:  6RW1 Ki: 1305 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.42α = 90
b = 41.49β = 104.54
c = 72.13γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

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