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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.45 kDa 
• Atom Count: 2286 
• Modelled Residue Count: 257 
• Deposited Residue Count: 257 
• Unique protein chains: 1

6UGN

Human Carbonic Anhydrase 2 complexed with SB4-205

• PDB DOI: 10.2210/pdb6UGN/pdb

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


• Deposited: 2019-09-26 Released: 2019-12-18 
• Deposition Author(s): Murray, A.B., Supuran, C.T., McKenna, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.173 
• R-Value Work: 0.150 
• R-Value Observed: 0.152 

Literature

"A Sweet Combination": Developing Saccharin and Acesulfame K Structures for Selectively Targeting the Tumor-Associated Carbonic Anhydrases IX and XII.

Bua, S., Lomelino, C., Murray, A.B., Osman, S.M., ALOthman, Z.A., Bozdag, M., Abdel-Aziz, H.A., Eldehna, W.M., McKenna, R., Nocentini, A., Supuran, C.T.

(2020) J Med Chem 63: 321-333

• PubMed: 31794211 
• DOI: 10.1021/acs.jmedchem.9b01669
• Primary Citation of Related Structures:  
  6U4Q, 6U4T, 6UGN, 6UGO, 6UGP, 6UGQ, 6UGR, 6UGZ, 6UH0


• PubMed Abstract: 
  

The sweeteners saccharin ( SAC ) and acesulfame K ( ACE ) recently entered the topic of anticancer human carbonic anhydrase (CA, EC 4.2.1.1) inhibitors, as they showed to selectively inhibit the tumor-associated CAs IX/XII over ubiquitous CAs. A drug design strategy is here reported, which took SAC and ACE as leads and produced a series of 2 H -benzo[ e ][1,2,4]thiadiazin-3(4 H )-one-1,1-dioxides ( BTD ). Many derivatives showed greater potency ( K _I s-CA IX 19.1-408.5 nM) and selectivity (II/IX SI 2-76) than the leads ( K _I s-CA IX 103, 2400 nM; II/IX-SI 56, >4) against CA IX/XII over off-target isoforms. A thorough X-ray crystallographic study depicted their binding mode to both CA II and IX-mimic. The most representative BTDs were characterized in vitro for their antitumor activity against A549, PC-3, and HCT-116 cancer cell lines both in normoxia and hypoxia. The two most effective compounds were assayed for their effect on several apoptosis markers, identifying promising leads for the development of new anticancer drugs.

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Organizational Affiliation: 

Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences , University of Florence , via Ugo Schiff 6 , 50019 Sesto Fiorentino, Florence , Italy.

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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q77 (Subject of Investigation/LOI)	C [auth A], D [auth A]	5,7-dimethyl-1lambda~6~,2,4-benzothiadiazine-1,1,3(2H,4H)-trione C9 H10 N2 O3 S OLDBDPLNTRFOOO-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Q77	Binding MOAD:  6UGN	Ki: 763.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.173 
• R-Value Work: 0.150 
• R-Value Observed: 0.152 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.471	α = 90
b = 41.481	β = 104.49
c = 71.83	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-09-26 
• Released Date: 2019-12-18 
Deposition Author(s): Murray, A.B., Supuran, C.T., McKenna, R.

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 1.1: 2020-01-22
  Changes: Database references