6CEH | pdb_00006ceh

Design, Synthesis, X-ray and Biological Activities of Selenides Bearing the Benzenesulfonamide Moiety as New Class of Agents for Prevention of Diabetic Cerebrovascular Pathology

• PDB DOI: https://doi.org/10.2210/pdb6CEH/pdb

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


• Deposited: 2018-02-11 Released: 2018-05-23 
• Deposition Author(s): Peat, T.S., Angeli, A., di Cesare Mannelli, L., Trallori, E., Ghelardini, C., Carta, F., Supuran, C.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Design, Synthesis, and X-ray of Selenides as New Class of Agents for Prevention of Diabetic Cerebrovascular Pathology.

Angeli, A., di Cesare Mannelli, L., Trallori, E., Peat, T.S., Ghelardini, C., Carta, F., Supuran, C.T.

(2018) ACS Med Chem Lett 9: 462-467

• PubMed: 29795760 
• DOI: https://doi.org/10.1021/acsmedchemlett.8b00076
• Primary Citation Related Structures: 
  6CEH


• PubMed Abstract: 
  

  A series of novel selenides bearing benzenesulfonamide moieties was synthesized and investigated for their inhibition on six human (h) carbonic anhydrase (CA, EC 4.2.1.1) isoforms such as the physiologically relevant hCA I, II, VA, VB, VII, and IX and the X-ray complex in adduct with hCA II for some of them investigated. These enzymes are involved in a variety of diseases including glaucoma, retinitis pigmentosa, epilepsy, arthritis, metabolic disorders, and cancer. The investigated compounds showed potent inhibitory action against hCA VA, VII, and IX, in the low nanomolar range, thus making them of interest for the development of isoform-selective inhibitors and as candidates for various biomedical applications.

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Organizational Affiliation: 
• University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
NEUROFARBA Department, Section of Pharmacology and Toxicology, Università degli Studi di Firenze, Viale Pieraccini 6, 50139 Florence, Italy.
CSIRO, 343 Royal Parade, Parkville, Victoria 3052, Australia.

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: 30.06 kDa 
• Atom Count: 2,553 
• Modeled Residue Count: 259 
• 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  Gene Names: CA2 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
EZ1	C [auth A], D [auth A]	4-[(prop-2-en-1-yl)selanyl]benzene-1-sulfonamide C9 H11 N O2 S Se KMBXWUNECGFGKU-UHFFFAOYSA-N
SO4	F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.452	α = 90
b = 41.485	β = 104.49
c = 72.455	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Peat, T.S., Angeli, A., di Cesare Mannelli, L., Trallori, E., Ghelardini, C., Carta, F., Supuran, C.T.

Revision History  

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2018-06-13
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description