6UFB

Carbonic anhydrase 2 with inhibitor (2Z)-2-benzylidene-3-oxo-N-(4-sulfamoylphenyl)butanamide (11a/D1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.151 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Discovery of Potent Dual-Tailed Benzenesulfonamide Inhibitors of Human Carbonic Anhydrases Implicated in Glaucoma and in Vivo Profiling of Their Intraocular Pressure-Lowering Action.

Fares, M.Eldehna, W.M.Bua, S.Lanzi, C.Lucarini, L.Masini, E.Peat, T.S.Abdel-Aziz, H.A.Nocentini, A.Keller, P.A.Supuran, C.T.

(2020) J Med Chem 63: 3317-3326

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b02090
  • Primary Citation of Related Structures:  
    6UFB, 6UFC, 6UFD

  • PubMed Abstract: 

    The design of three dual-tailed sulfonamide series 11a-11g , 14a-14h , and 16a-16e as carbonic anhydrase (CA, EC 4.2.1.1) inhibitors are presented. All compounds were evaluated for inhibitory action against pharmacologically relevant human CA isoforms I, II, IV, and VII. Compounds 11a-11g emerged as potent CA inhibitors against the four tested isoforms with a significant selectivity to CA II, which is implicated in glaucoma ( K i in the range 0.36-6.9 nM). X-ray crystallographic analysis of three compounds ( 11a , 11d , and 11g ) bound to CA II showed the validity of the adopted drug design strategy as specific moieties within the ligand structure interacted directly with the hydrophobic and hydrophilic halves of the CA II active site. Compounds 11b - 11d and 11g were evaluated for their intraocular pressure-lowering effects in a rabbit model of glaucoma. 11b and 11d showed significant efficacy when compared to the clinically used drug dorzolamide.


  • Organizational Affiliation

    School of Chemistry & Molecular Bioscience, Molecular Horizons, and Illawarra Health & Medical Research Institute, University of Wollongong, Wollongong, NSW 2522, Australia.


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
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q64 (Subject of Investigation/LOI)
Query on Q64

Download Ideal Coordinates CCD File 
E [auth A](2Z)-2-benzylidene-3-oxo-N-(4-sulfamoylphenyl)butanamide
C17 H16 N2 O4 S
NDDZSPLPKNIELX-WJDWOHSUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
SO4 BindingDB:  6UFB Ki: min: 8.90e+7, max: 3.00e+8 (nM) from 4 assay(s)
CL BindingDB:  6UFB Ki: min: 2.00e+8, max: 2.00e+8 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.356α = 90
b = 41.485β = 104.528
c = 72.028γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2020-08-05 
  • Deposition Author(s): Peat, T.S.

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description