6GOT

Crystal structure of human carbonic anhydrase II in complex with the inhibitor 4-(phenethylthio)benzenesulfonamide

• PDB DOI: https://doi.org/10.2210/pdb6GOT/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2018-06-04 Released: 2018-10-03 
• Deposition Author(s): Ferraroni, M., Supuran, C.T., Angeli, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.223 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 

Literature

Synthesis of different thio-scaffolds bearing sulfonamide with subnanomolar carbonic anhydrase II and IX inhibitory properties and X-ray investigations for their inhibitory mechanism.

Angeli, A., Tanini, D., Capperucci, A., Malevolti, G., Turco, F., Ferraroni, M., Supuran, C.T.

(2018) Bioorg Chem 81: 642-648

• PubMed: 30253337 
• DOI: https://doi.org/10.1016/j.bioorg.2018.09.028
• Primary Citation of Related Structures:  
  6GOT


• PubMed Abstract: 
  

  Several new molecules with different thio-scaffolds were designed, synthesised, and evaluated biologically as inhibitors of Carbonic Anhydrases (CAIs). The structure-activity relationship analysis identified thioether derivatives, here reported, as a potent and selective CAIs against hCA II and hCA IX. High resolution X-ray structure of inhibitor bound hCA II revealed extensive interactions with the hydrophobic pocket of active site and provided molecular insight into the binding properties of these new inhibitors.

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Organizational Affiliation: 

Department of University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 29.83 kDa 
• Atom Count: 2,218 
• Modelled Residue Count: 257 
• 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  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
F6W	E [auth A]	4-(2-phenylethylsulfanyl)benzenesulfonamide C14 H15 N O2 S2 BIDLYFNXVUUEMA-UHFFFAOYSA-N
GOL	C [auth A], D [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
F6W	Binding MOAD:  6GOT	Ki: 0.4 (nM) from 1 assay(s)
	BindingDB:  6GOT	Kd: 25 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.223 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.443	α = 90
b = 41.284	β = 104.38
c = 72.171	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Ferraroni, M., Supuran, C.T., Angeli, A.

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2018-10-10
  Changes: Data collection, Structure summary
• Version 1.2: 2024-01-17
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary