6Z04

Nido-carborane butyl-sulfonamide in complex with CA IX mimic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

The structural basis for the selectivity of sulfonamido dicarbaboranes toward cancer-associated carbonic anhydrase IX.

Kugler, M.Holub, J.Brynda, J.Pospisilova, K.Anwar, S.E.Bavol, D.Havranek, M.Kral, V.Fabry, M.Gruner, B.Rezacova, P.

(2020) J Enzyme Inhib Med Chem 35: 1800-1810

  • DOI: https://doi.org/10.1080/14756366.2020.1816996
  • Primary Citation of Related Structures:  
    6YZJ, 6YZK, 6YZL, 6YZM, 6YZN, 6YZO, 6YZP, 6YZQ, 6YZR, 6YZS, 6YZT, 6YZU, 6YZV, 6YZW, 6YZX, 6Z04

  • PubMed Abstract: 

    Human carbonic anhydrase IX (CA IX), a protein specifically expressed on the surface of solid tumour cells, represents a validated target both for anticancer therapy and diagnostics. We recently identified sulfonamide dicarbaboranes as promising inhibitors of CA IX with favourable activities both in vitro and in vivo . To explain their selectivity and potency, we performed detailed X-ray structural analysis of their interactions within the active sites of CA IX and CA II. Series of compounds bearing various aliphatic linkers between the dicarbaborane cluster and sulfonamide group were examined. Preferential binding towards the hydrophobic part of the active site cavity was observed. Selectivity towards CA IX lies in the shape complementarity of the dicarbaborane cluster with a specific CA IX hydrophobic patch containing V131 residue. The bulky side chain of F131 residue in CA II alters the shape of the catalytic cavity, disrupting favourable interactions of the spherical dicarbaborane cluster.


  • Organizational Affiliation

    Deparment of Structural Biology, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo sapiensMutation(s): 7 
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.035α = 90
b = 41.345β = 103.98
c = 72.682γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
FFTphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech RepublicGA15-05677S
Other governmentCzech RepublicTE01020028

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 2.0: 2020-11-04
    Changes: Non-polymer description, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description