6HWZ | pdb_00006hwz

Selenols: a new class of Carbonic Anhydrase inhibitors

• PDB DOI: https://doi.org/10.2210/pdb6HWZ/pdb

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


• Deposited: 2018-10-15 Released: 2018-12-26 
• Deposition Author(s): Angeli, A., Ferraroni, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Selenols: a new class of carbonic anhydrase inhibitors.

Angeli, A., Tanini, D., Nocentini, A., Capperucci, A., Ferraroni, M., Gratteri, P., Supuran, C.T.

(2019) Chem Commun (Camb) 55: 648-651

• PubMed: 30560259 
• DOI: https://doi.org/10.1039/c8cc08562e
• Primary Citation of Related Structures:  
  6HWZ, 6HX5, 6SWM


• PubMed Abstract: 
  

  Stable aryl selenols were obtained through a convenient procedure. Selenols represent a new chemotype acting as carbonic anhydrase inhibitors (CAIs), inhibiting four human isoforms, CAs I, II, VII and the tumor-associated CA IX. X-ray crystallographic, physical and computational studies provided insights into the binding mode of this conceptually new class of CAIs.

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Organizational Affiliation: 

University of Florence, NEUROFARBA Department, Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy. [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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.26 kDa 
• Atom Count: 4,140 
• Modelled Residue Count: 512 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 1	A, B	261	Homo sapiens	Mutation(s): 0  Gene Names: CA1 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00915 (Homo sapiens) Explore P00915  Go to UniProtKB:  P00915
PHAROS:  P00915 GTEx:  ENSG00000133742

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GXE	D [auth A], F [auth B]	benzeneselenol C6 H6 Se WDODWFPDZYSKIA-UHFFFAOYSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GXE	BindingDB:  6HWZ	Ki: 280 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.38	α = 90
b = 71.527	β = 90
c = 120.695	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Angeli, A., Ferraroni, M.

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 1.1: 2019-01-23
  Changes: Data collection, Database references
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references