3V5G

Crystal structure of human carbonic anhydrase II in complex with the 4-sulfamido-benzenesulfonamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Development of potent carbonic anhydrase inhibitors incorporating both sulfonamide and sulfamide groups.

D'Ambrosio, K.Smaine, F.Z.Carta, F.De Simone, G.Winum, J.Y.Supuran, C.T.

(2012) J.Med.Chem. 55: 6776-6783

  • DOI: 10.1021/jm300818k

  • PubMed Abstract: 
  • A series of compounds incorporating both sulfonamide and sulfamide as zinc-binding groups (ZBGs) are reported as inhibitors of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1). Crystallographic studies on the complex of hCA II with the lead comp ...

    A series of compounds incorporating both sulfonamide and sulfamide as zinc-binding groups (ZBGs) are reported as inhibitors of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1). Crystallographic studies on the complex of hCA II with the lead compound of this series, namely, 4-sulfamido-benzenesulfonamide, revealed the binding of two molecules in the enzyme active site cavity, the first one canonically coordinated to the zinc ion by means of the sulfonamide group and the second one located at the entrance of the cavity. This observation led to the design of elongated molecules incorporating these two ZBGs, separated by a linker of proper length, to allow the simultaneous binding to these different sites. The "long" inhibitors indeed showed around 10 times better enzyme inhibitory properties as compared to the shorter molecules against four physiologically relevant human (h) isoforms, hCA I, II, IX, and XII.


    Organizational Affiliation

    Istituto di Biostrutture e Bioimmagini-CNR , via Mezzocannone 16, 80134 Napoli, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
260Homo sapiensGene 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MBO
Query on MBO

Download SDF File 
Download CCD File 
A
MERCURIBENZOIC ACID
C7 H5 Hg O2
FVFZSVRSDNUCGG-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
0F3
Query on 0F3

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Download CCD File 
A
4-(sulfamoylamino)benzenesulfonamide
C6 H9 N3 O4 S2
VORWCQRDADUXEU-UHFFFAOYSA-N
 Ligand Interaction
HGB
Query on HGB

Download SDF File 
Download CCD File 
A
4-(HYDROXYMERCURY)BENZOIC ACID
C7 H6 Hg O3
WMHRYLDWLOGHSG-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0F3Ki: 74 - 123 nM (100) BINDINGDB
0F3Ki: 74 nM BINDINGMOAD
0F3Ki: 74 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.250α = 90.00
b = 41.350β = 104.36
c = 71.960γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2012-08-22
    Type: Database references