6SDT

HUMAN CARBONIC ANHYDRASE VII IN COMPLEX WITH A SULFONAMIDE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

Starting Model: experimental
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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 7274Homo sapiensMutation(s): 2 
Gene Names: CA7
EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P43166 (Homo sapiens)
Explore P43166 
Go to UniProtKB:  P43166
PHAROS:  P43166
GTEx:  ENSG00000168748 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43166
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
L8N BindingDB:  6SDT Ki: 16 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.28α = 90
b = 89.36β = 90
c = 44.165γ = 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