4E3D

Nucleophile recognition as an alternative inhibition mode for benzoic acid based carbonic anhydrase inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MBOClick on this verticalbar to view detailsBest fitted GTQClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Nucleophile recognition as an alternative inhibition mode for benzoic acid based carbonic anhydrase inhibitors

Martin, D.P.Cohen, S.M.

(2012) Chem Commun (Camb) 48: 5259-5261

  • DOI: https://doi.org/10.1039/c2cc32013d
  • Primary Citation of Related Structures:  
    4E3D, 4E3F, 4E3G, 4E3H, 4E49, 4E4A

  • PubMed Abstract: 

    A series of hydroxybenzoic acid derivatives have shown inhibitory activity against carbonic anhydrase (CA). X-ray crystallography shows that these molecules inhibit not by binding the active site metal ion but by strong hydrogen bonding to the metal-bound water nucleophile. The binding mode observed for these molecules is distinct when compared to other non-metal-binding CA inhibitors.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, USA.


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 (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
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
GTQ BindingDB:  4E3D Ki: 4100 (nM) from 1 assay(s)
IC50: 5.00e+6 (nM) from 1 assay(s)
PDBBind:  4E3D IC50: 5.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.204α = 90
b = 41.479β = 104.32
c = 72.119γ = 90
Software Package:
Software NamePurpose
APEXdata collection
PHASERphasing
REFMACrefinement
APEXdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MBOClick on this verticalbar to view detailsBest fitted GTQClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2012-06-27 
  • Deposition Author(s): Cohen, S.M.

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description