5FDI | pdb_00005fdi

Crystal structure of Human Carbonic Anhydrase II with the anticonvulsant sulfamide JNJ-26990990 and its S,S-dioxide analog.

• PDB DOI: https://doi.org/10.2210/pdb5FDI/pdb

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


• Deposited: 2015-12-16 Released: 2016-05-18 
• Deposition Author(s): Di Fiore, A., De Simone, G., Alterio, V., Riccio, V., Winum, J.-Y., Carta, F., Supuran, C.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.158 (DCC) 

Starting Model: experimental

Literature

The anticonvulsant sulfamide JNJ-26990990 and its S,S-dioxide analog strongly inhibit carbonic anhydrases: solution and X-ray crystallographic studies.

Di Fiore, A., De Simone, G., Alterio, V., Riccio, V., Winum, J.Y., Carta, F., Supuran, C.T.

(2016) Org Biomol Chem 14: 4853-4858

• PubMed: 27151329 
• DOI: https://doi.org/10.1039/c6ob00803h
• Primary Citation Related Structures: 
  5FDC, 5FDI


• PubMed Abstract: 
  

  JNJ-26990990 ((benzo[b]thien-3-yl)methyl)sulfamide, a sulfamide derivative structurally related to the antiepileptic drug zonisamide, was reported to be devoid of carbonic anhydrase (CA, EC 4.2.1.1) inhibitory properties. Here we report that JNJ-26990990 and its S,S-dioxide analog significantly inhibit six human (h) isoforms, hCA I, II, VII, IX, XII and XIV, involved in crucial physiological processes. Inhibition and X-ray crystallographic data for the binding of the two compounds to these enzymes show significant similarity with the zonisamide inhibitory pattern. These findings prompted us to reconsider the structural/pharmacological requirements for designing effective antiepileptics possessing zinc-binding groups of the sulfamide, sulfamate or sulfonamide type in their molecules.

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Organizational Affiliation: 
• Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy. [e-mail] [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: 30.06 kDa 
• Atom Count: 2,352 
• 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  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
HGB	E [auth A]	4-(HYDROXYMERCURY)BENZOIC ACID C7 H6 Hg O3 WMHRYLDWLOGHSG-UHFFFAOYSA-M
5WM	C [auth A]	1,1-bis(oxidanylidene)-3-[(sulfamoylamino)methyl]-1-benzothiophene C9 H10 N2 O4 S2 KCPWPUJVAMOFBB-UHFFFAOYSA-N
GOL	D [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: 1.85 Å
• R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.158 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.006	α = 90
b = 41.282	β = 104.16
c = 71.981	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data reduction
HKL-2000	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-18 
Deposition Author(s): Di Fiore, A., De Simone, G., Alterio, V., Riccio, V., Winum, J.-Y., Carta, F., Supuran, C.T.

Revision History  

• Version 1.0: 2016-05-18
  Type: Initial release
  
• Version 1.1: 2016-06-01
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description