5WEX | pdb_00005wex

Discovery of new selenoureido analogs of 4-(4-fluorophenylureido) benzenesulfonamides as carbonic anhydrase inhibitors

• PDB DOI: https://doi.org/10.2210/pdb5WEX/pdb

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


• Deposited: 2017-07-10 Released: 2017-10-11 
• Deposition Author(s): Angeli, A., Tanini, D., Peat, T.S., Di Cesare Mannelli, L., Bartolucci, G., Capperucci, A., Ghelardini, C., Supuran, C.T., Carta, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 
  0.147 (Depositor), 0.147 (DCC) 
• R-Value Work: 
  0.118 (Depositor), 0.118 (DCC) 
• R-Value Observed: 
  0.119 (Depositor) 

Literature

Discovery of New Selenoureido Analogues of 4-(4-Fluorophenylureido)benzenesulfonamide as Carbonic Anhydrase Inhibitors.

Angeli, A., Tanini, D., Peat, T.S., Di Cesare Mannelli, L., Bartolucci, G., Capperucci, A., Ghelardini, C., Supuran, C.T., Carta, F.

(2017) ACS Med Chem Lett 8: 963-968

• PubMed: 28947945 
• DOI: https://doi.org/10.1021/acsmedchemlett.7b00280
• Primary Citation Related Structures: 
  5ULN, 5UMC, 5WEX


• PubMed Abstract: 
  

  A series of benzenesulfonamides bearing selenourea moieties was obtained considering the ureido-sulfonamide SLC-0111 , in Phase I clinical trials as antitumor agent, as a lead molecule. All compounds showed interesting inhibition potencies against the physiologically relevant human (h) carbonic anhydrase (hCAs, EC 4.2.1.1) isoforms I, II, IV, and IX. The most flexible analogues in the series 14 - 19 showed low nanomolar inhibition constants against hCA I, II, and IX. We assessed selected compounds on the in vitro antioxidant properties and binding modes and evaluated ex vivo human prostate (PC3), breast (MDA-MB-231), and colon-rectal (HT-29) cancer cell lines both in normoxic and hypoxic conditions.

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Organizational Affiliation: 
• University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
University of Florence, Department of Chemistry "Ugo Schiff", Via della Lastruccia 13, I-50019 Sesto Fiorentino, Florence, Italy.
CSIRO, 343 Royal Parade, Parkville, Victoria 3052, Australia.
NEUROFARBA Department, Section of Pharmacology and Toxicology, Università degli Studi di Firenze, Viale Pieraccini 6, 50139 Florence, Italy.

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: 29.85 kDa 
• Atom Count: 2,464 
• Modeled Residue Count: 258 
• Deposited Residue Count: 260 
• Unique protein chains: 1

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 (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
8JS	D [auth A]	4-{[(4-fluorophenyl)carbamothioyl]amino}benzene-1-sulfonamide C13 H12 F N3 O2 S2 VUDOFEJVAFMLEC-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	E [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
8JS	BindingDB:  5WEX	Ki: 14 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free:  0.147 (Depositor), 0.147 (DCC) 
• R-Value Work:  0.118 (Depositor), 0.118 (DCC) 
• R-Value Observed: 0.119 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.472	α = 90
b = 41.502	β = 104.39
c = 72.35	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Angeli, A., Tanini, D., Peat, T.S., Di Cesare Mannelli, L., Bartolucci, G., Capperucci, A., Ghelardini, C., Supuran, C.T., Carta, F.

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references