Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.67 kDa 
• Atom Count: 2332 
• Modelled Residue Count: 257 
• Deposited Residue Count: 257 
• Unique protein chains: 1

5SZ3

Carbonic anhydrase II in complex with 4-(3-quinolinyl)-benzenesulfonamide

• PDB DOI: 10.2210/pdb5SZ3/pdb

• Classification: Lyase/Lyase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-08-12 Released: 2016-12-21 
• Deposition Author(s): Bhatt, A., Mahon, B.P., Cornelio, B., McKenna, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.203 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

Structure-Activity Relationships of Benzenesulfonamide-Based Inhibitors towards Carbonic Anhydrase Isoform Specificity.

Bhatt, A., Mahon, B.P., Cruzeiro, V.W., Cornelio, B., Laronze-Cochard, M., Ceruso, M., Sapi, J., Rance, G.A., Khlobystov, A.N., Fontana, A., Roitberg, A., Supuran, C.T., McKenna, R.

(2017) Chembiochem 18: 213-222

• PubMed: 27860128 
• DOI: 10.1002/cbic.201600513
• Primary Citation of Related Structures:  
  5SZ0, 5SZ1, 5SZ2, 5SZ3, 5SZ4, 5SZ5, 5SZ6, 5SZ7


• PubMed Abstract: 
  

Carbonic anhydrases (CAs) are implicated in a wide range of diseases, including the upregulation of isoforms CA IX and XII in many aggressive cancers. However, effective inhibition of disease-implicated CAs should minimally affect the ubiquitously expressed isoforms, including CA I and II, to improve directed distribution of the inhibitors to the cancer-associated isoforms and reduce side effects. Four benzenesulfonamide-based inhibitors were synthesized by using the tail approach and displayed nanomolar affinities for several CA isoforms. The crystal structures of the inhibitors bound to a CA IX mimic and CA II are presented. Further in silico modeling was performed with the inhibitors docked into CA I and XII to identify residues that contributed to or hindered their binding interactions. These structural studies demonstrated that active-site residues lining the hydrophobic pocket, especially positions 92 and 131, dictate the positional binding and affinity of inhibitors, whereas the tail groups modulate CA isoform specificity. Geometry optimizations were performed on each ligand in the crystal structures and showed that the energetic penalties of the inhibitor conformations were negligible compared to the gains from active-site interactions. These studies further our understanding of obtaining isoform specificity when designing small molecule CA inhibitors.

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Organizational Affiliation: 

Department of, Biochemistry and Molecular Biology, College of Medicine, University of Florida, P. O. Box 100245, Gainesville, FL, 32610, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	257	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
72H	H [auth A]	4-(3-quinolinyl)-benzenesulfonamide C15 H12 N2 O2 S HGZKFXIUXSUJHM-UHFFFAOYSA-N
DMS	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
72H	BindingDB:  5SZ3	Ki: min: 0.2, max: 2.5 (nM) from 2 assay(s)
	Binding MOAD:  5SZ3	Ki: 2.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.203 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.303	α = 90
b = 41.379	β = 104.37
c = 71.916	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-08-12 
• Released Date: 2016-12-21 
Deposition Author(s): Bhatt, A., Mahon, B.P., Cornelio, B., McKenna, R.

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2016-12-28
  Changes: Database references
• Version 1.2: 2017-02-01
  Changes: Database references