4PQ7

The crystal structure of the human carbonic anhydrase ii in complex with a sulfamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Hydrophobic substituents of the phenylmethylsulfamide moiety can be used for the development of new selective carbonic anhydrase inhibitors.

De Simone, G.Pizika, G.Monti, S.M.Di Fiore, A.Ivanova, J.Vozny, I.Trapencieris, P.Zalubovskis, R.Supuran, C.T.Alterio, V.

(2014) Biomed Res Int 2014: 523210-523210

  • DOI: 10.1155/2014/523210

  • PubMed Abstract: 
  • A new series of compounds containing a sulfamide moiety as zinc-binding group (ZBG) has been synthesized and tested for determining inhibitory properties against four human carbonic anhydrase (hCA) isoforms, namely, CAs I, II, IX, and XII. The X-ray ...

    A new series of compounds containing a sulfamide moiety as zinc-binding group (ZBG) has been synthesized and tested for determining inhibitory properties against four human carbonic anhydrase (hCA) isoforms, namely, CAs I, II, IX, and XII. The X-ray structure of the cytosolic dominant isoform hCA II in complex with the best inhibitor of the series has also been determined providing further insights into sulfamide binding mechanism and confirming that such zinc-binding group, if opportunely derivatized, can be usefully exploited for obtaining new potent and selective CAIs. The analysis of the structure also suggests that for drug design purposes the but-2-yn-1-yloxy moiety tail emerges as a very interesting substituent of the phenylmethylsulfamide moiety due to its capability to establish strong van der Waals interactions with a hydrophobic cleft on the hCA II surface, delimited by residues Phe131, Val135, Pro202, and Leu204. Indeed, the complementarity of this tail with the cleft suggests that different substituents could be used to discriminate between isoforms having clefts with different sizes.


    Organizational Affiliation

    Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Naples, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
262Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to Gene View: CA2
Go to UniProtKB:  P00918
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IL3
Query on IL3

Download SDF File 
Download CCD File 
A
1-but-2-ynoxy-4-[(sulfamoylamino)methyl]benzene
C11 H14 N2 O3 S
YCDIYRUTYILYGJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IL3Ki: 9.5 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.397α = 90.00
b = 41.342β = 104.29
c = 71.798γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CrystalCleardata collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-08
    Type: Initial release