6H37

The crystal structure of human carbonic anhydrase VII in complex with 4-(4-phenyl)-4-hydroxy-1-piperidine-1-carbonyl)benzenesulfonamide

• PDB DOI:  https://doi.org/10.2210/pdb6H37/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-07-17 Released: 2018-12-19 
• Deposition Author(s): Buemi, M.R., Di Fiore, A., De Luca, L., Ferro, S., Mancuso, F., Monti, S.M., Buonanno, M., Angeli, A., Russo, E., De Sarro, G., Supuran, C.T., De Simone, G., Gitto, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.194 

Literature

Exploring structural properties of potent human carbonic anhydrase inhibitors bearing a 4-(cycloalkylamino-1-carbonyl)benzenesulfonamide moiety.

Buemi, M.R., Di Fiore, A., De Luca, L., Angeli, A., Mancuso, F., Ferro, S., Monti, S.M., Buonanno, M., Russo, E., De Sarro, G., De Simone, G., Supuran, C.T., Gitto, R.

(2018) Eur J Med Chem 163: 443-452

• PubMed: 30530195 
• DOI: https://doi.org/10.1016/j.ejmech.2018.11.073
• Primary Citation of Related Structures:  
  6H2Z, 6H33, 6H34, 6H36, 6H37, 6H38


• PubMed Abstract: 
  

Guided by the crystal structure of 4-(3,4-dihydroquinolin-1(2H)-ylcarbonyl)benzenesulfonamide 3 in complex with hCA II (PDB code 4Z0Q), a novel series of cycloalkylamino-1-carbonylbenzenesulfonamides was designed and synthesized. Thus, we replaced the quinoline ring with an azepine/piperidine/piperazine nucleus and introduced further modifications on cycloalkylamine nucleus by means the installation of hydrophobic/hydrophilic functionalities able to establish additional contacts in the middle area of the enzyme cavity. Among the synthesized compounds, the derivatives 7a, 7b, 8b exhibited a remarkable inhibition for hCA II and the brain-expressed hCA VII in subnanomolar range. The binding of these molecules to the target enzymes was characterized by means of a crystallographic analysis, providing a clear snapshot of the most important interactions established by this class of inhibitors into the hCA II and hCA VII catalytic site. Notably, our results showed that the benzylpiperazine tail of compound 8b is oriented both in hCA II and in hCA VII toward a poorly explored region of the active site. These features should be further investigated for the design of new isoform selective CA inhibitors.

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Organizational Affiliation: 

Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), Università degli Studi di Messina, Viale Palatucci, Polo didattico SS, Annunziata, 98168, Messina, Italy. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 31.35 kDa 
• Atom Count: 2,197 
• Modelled Residue Count: 258 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 7	A	274	Homo sapiens	Mutation(s): 2  Gene Names: CA7 EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P43166 (Homo sapiens) Explore P43166  Go to UniProtKB:  P43166
PHAROS:  P43166

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FKQ	C [auth A]	4-(4-oxidanyl-4-phenyl-piperidin-1-yl)carbonylbenzenesulfonamide C18 H20 N2 O4 S XEMCUUOBNNOBLG-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FKQ	Binding MOAD:  6H37	Ki: 2.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.194 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.04	α = 90
b = 88.64	β = 90
c = 44.11	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-19 
Deposition Author(s): Buemi, M.R., Di Fiore, A., De Luca, L., Ferro, S., Mancuso, F., Monti, S.M., Buonanno, M., Angeli, A., Russo, E., De Sarro, G., Supuran, C.T., De Simone, G., Gitto, R.

Revision History  

• Version 1.0: 2018-12-19
  Type: Initial release