6SDS

HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH A SULFONAMIDE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Phenyl(thio)phosphon(amid)ate Benzenesulfonamides as Potent and Selective Inhibitors of Human Carbonic Anhydrases II and VII Counteract Allodynia in a Mouse Model of Oxaliplatin-Induced Neuropathy.

Nocentini, A.Alterio, V.Bua, S.Micheli, L.Esposito, D.Buonanno, M.Bartolucci, G.Osman, S.M.ALOthman, Z.A.Cirilli, R.Pierini, M.Monti, S.M.Di Cesare Mannelli, L.Gratteri, P.Ghelardini, C.De Simone, G.Supuran, C.T.

(2020) J Med Chem 63: 5185-5200

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b02135
  • Primary Citation of Related Structures:  
    6SDS, 6SDT

  • PubMed Abstract: 

    Human carbonic anhydrase (CA; EC 4.2.1.1) isoforms II and VII are implicated in neuronal excitation, seizures, and neuropathic pain (NP). Their selective inhibition over off-target CAs is expected to produce an anti-NP action devoid of side effects due to promiscuous CA modulation. Here, a drug design strategy based on the observation of (dis)similarities between the target CA active sites was planned with benzenesulfonamide derivatives and, for the first time, a phosphorus-based linker. Potent and selective CA II/VII inhibitors were identified among the synthesized phenyl(thio)phosphon(amid)ates 3 - 22 . X-ray crystallography depicted the binding mode of phosphonic acid 3 to both CAs II and VII. The most promising derivatives, after evaluation of their stability in acidic media, were tested in a mouse model of oxaliplatin-induced neuropathy. The most potent compound racemic mixture was subjected to HPLC enantioseparation, and the identification of the eutomer, the ( S )-enantiomer, allowed to halve the dose totally relieving allodynia in mice.


  • Organizational Affiliation

    Department of NEUROFARBA, Pharmaceutical and Nutraceutical Section, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
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
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
L8N Binding MOAD:  6SDS Ki: 37.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.224α = 90
b = 41.241β = 104.11
c = 71.946γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description