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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 30.18 kDa 
• Atom Count: 2671 
• Modelled Residue Count: 259 
• Deposited Residue Count: 260 
• Unique protein chains: 1

6ODZ

Benzensulfonamides bearing spyrohydantoin moieties act as potent inhibitors of human carbonic anhydrases II and VII and show neuropathic pain attenuating effects

• PDB DOI: 10.2210/pdb6ODZ/pdb

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


• Deposited: 2019-03-27 Released: 2019-06-12 
• Deposition Author(s): Peat, T.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.145 
• R-Value Work: 0.120 
• R-Value Observed: 0.121 

Literature

Benzensulfonamides bearing spyrohydantoin moieties act as potent inhibitors of human carbonic anhydrases II and VII and show neuropathic pain attenuating effects.

Angeli, A., Di Cesare Mannelli, L., Ghelardini, C., Peat, T.S., Bartolucci, G., Menicatti, M., Carta, F., Supuran, C.T.

(2019) Eur J Med Chem 177: 188-197

• PubMed: 31136893 
• DOI: 10.1016/j.ejmech.2019.05.058
• Primary Citation of Related Structures:  
  6ODZ, 6OE0, 6OE1


• PubMed Abstract: 
  

Carbonic Anhydrases have been recently validated as novel therapeutic targets in neuropathic pain. In this study, we combine the anticonvulsant propriety of spyrohydantoin and the CA inhibitor moiety of benzenesulfonamide to synthesize a novel series of spyrohydantoin bearing sulfonamides with strong activity against hCA II and VII. These isoforms are present in the nervous system and largely expressed both at the central as well as at peripheral level and can be modulated for pain relief. The crystal structures of hCA II in complex with selected compounds 5a-c demonstrate the importance of the tail in the binding modes within the isoform. Finally, in vivo, in an animal model of oxaliplatin induced neuropathy, compounds with organoselenium tails (8b-c) showed potent neuropathic pain attenuating effects. Taken together, these data strongly suggest the translational utility of these inhibitors as novel pain relievers.

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Organizational Affiliation: 

University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Florence, Italy. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	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
M8J	C [auth A], D [auth A]	2-(2,4-dioxo-1,3-diazaspiro[4.4]nonan-3-yl)-N-(4-sulfamoylphenyl)acetamide C15 H18 N4 O5 S PWGCLXASZRXSOJ-UHFFFAOYSA-N
GOL	E [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
M8J	Binding MOAD:  6ODZ	Ki: 0.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.145 
• R-Value Work: 0.120 
• R-Value Observed: 0.121 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.289	α = 90
b = 41.428	β = 104.39
c = 72.223	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-03-27 
• Released Date: 2019-06-12 
Deposition Author(s): Peat, T.S.

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release