3T5U

Crystal structure of the human carbonic anhydrase II in complex with N-hydroxy benzenesulfonamide

• PDB DOI: https://doi.org/10.2210/pdb3T5U/pdb

• Classification: LYASE/LYASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2011-07-28 Released: 2012-06-20 
• Deposition Author(s): Di Fiore, A., Maresca, A., Alterio, V., Supuran, C.T., De Simone, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.183 
• R-Value Work: 0.171 

Starting Model: experimental

Literature

Carbonic anhydrase inhibitors: X-ray crystallographic studies for the binding of N-substituted benzenesulfonamides to human isoform II.

Di Fiore, A., Maresca, A., Alterio, V., Supuran, C.T., De Simone, G.

(2011) Chem Commun (Camb) 47: 11636-11638

• PubMed: 21952494 
• DOI: https://doi.org/10.1039/c1cc14575d
• Primary Citation of Related Structures:  
  3T5U, 3T5Z


• PubMed Abstract: 
  

  N-substituted benzenesulfonamides, incorporating the N-amino-, N-hydroxy- and N-methoxy-moieties at the sulfonamide zinc binding group, have been investigated as CAIs by means of inhibition and structural studies, unraveling interesting aspects related to their inhibition mechanism.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.33 kDa 
• Atom Count: 2,402 
• Modelled Residue Count: 257 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	259	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MBO	H [auth A]	MERCURIBENZOIC ACID C7 H5 Hg O2 FVFZSVRSDNUCGG-UHFFFAOYSA-N
A09	C [auth A], D [auth A], E [auth A], F [auth A]	N-hydroxybenzenesulfonamide C6 H7 N O3 S BRMDATNYMUMZLN-UHFFFAOYSA-N
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
A09	PDBBind:  3T5U	Ki: 26 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.183 
• R-Value Work: 0.171 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.26	α = 90
b = 41.54	β = 104.43
c = 72.09	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-20 
Deposition Author(s): Di Fiore, A., Maresca, A., Alterio, V., Supuran, C.T., De Simone, G.

Revision History  

• Version 1.0: 2012-06-20
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description