4YX4

Human Carbonic Anhydrase II complexed with an inhibitor with a benzenesulfonamide group (1).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Kinetic and Structural Insights into the Mechanism of Binding of Sulfonamides to Human Carbonic Anhydrase by Computational and Experimental Studies.

Gaspari, R.Rechlin, C.Heine, A.Bottegoni, G.Rocchia, W.Schwarz, D.Bomke, J.Gerber, H.D.Klebe, G.Cavalli, A.

(2016) J.Med.Chem. 59: 4245-4256

  • DOI: 10.1021/acs.jmedchem.5b01643
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The binding of sulfonamides to human carbonic anhydrase II (hCAII) is a complex and long-debated example of protein-ligand recognition and interaction. In this study, we investigate the para-substituted n-alkyl and hydroxyethylene-benzenesulfonamides ...

    The binding of sulfonamides to human carbonic anhydrase II (hCAII) is a complex and long-debated example of protein-ligand recognition and interaction. In this study, we investigate the para-substituted n-alkyl and hydroxyethylene-benzenesulfonamides, providing a complete reconstruction of their binding pathway to hCAII by means of large-scale molecular dynamics simulations, density functional calculations, surface plasmon resonance (SPR) measurements, and X-ray crystallography experiments. Our analysis shows that the protein-ligand association rate (kon) dramatically increases with the ligand's hydrophobicity, pointing to the existence of a prebinding stage largely stabilized by a favorable packing of the ligand's apolar moieties with the hCAII "hydrophobic wall". The characterization of the binding pathway allows an unprecedented understanding of the structure-kinetic relationship in hCAII/benzenesulfonamide complexes, depicting a paradigmatic scenario for the multistep binding process in protein-ligand systems.


    Organizational Affiliation

    Department of Drug Discovery and Development, Istituto Italiano di Tecnologia , 16163 Genova, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
260Homo 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 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
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FB2
Query on FB2

Download SDF File 
Download CCD File 
A
benzenesulfonamide
C6 H7 N O2 S
KHBQMWCZKVMBLN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FB2Ki: 305 - 5870 nM (100) BINDINGDB
FB2Kd: 660 - 1149700 nM (100) BINDINGDB
FB2Kd: 1135 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.385α = 90.00
b = 41.508β = 104.43
c = 72.254γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union / ERC268145-DrugProfilBind

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-05-25
    Type: Database references