6UFC

Carbonic anhydrase 2 with inhibitor (2Z)-2-[(4-methoxyphenyl)methylidene]-3-oxo-N-(4-sulfamoylphenyl)butanamide (11d/D4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.117 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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: 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 ...

    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

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 2A260Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Q6A (Subject of Investigation/LOI)
Query on Q6A

Download Ideal Coordinates CCD File 
C [auth A](2Z)-2-[(4-methoxyphenyl)methylidene]-3-oxo-N-(4-sulfamoylphenyl)butanamide
C18 H18 N2 O5 S
BNJYMFAWZKZPKJ-BOPFTXTBSA-N
 Ligand Interaction
GOL
Query on GOL

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

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

Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
Q6A Binding MOAD:  6UFC Ki: 0.45 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.117 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.561α = 90
b = 41.518β = 104.72
c = 72.412γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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