6GOT | pdb_00006got

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 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

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 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.
Department of University of Florence, Department of Chemistry "Ugo Schiff", Via della Lastruccia 13, I-50019 Sesto Fiorentino, Italy.
Department of University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy. Electronic address: [e-mail].

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 
• Modeled 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 (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 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	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 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

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