6YQT | pdb_00006yqt

CRYSTAL STRUCTURE OF HUMAN CA II IN COMPLEX WITH A SULFONAMIDE DERIVATIVE OF 2-MERCAPTOBENZOXAZOLE

• PDB DOI: https://doi.org/10.2210/pdb6YQT/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-04-18 Released: 2020-07-01 
• Deposition Author(s): Alterio, V., De Simone, G., Esposito, D.
• Funding Organization(s): Italian Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.206 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.170 (DCC) 

Starting Model: experimental

Literature

2-Mercaptobenzoxazoles: a class of carbonic anhydrase inhibitors with a novel binding mode to the enzyme active site.

Bozdag, M., Supuran, C.T., Esposito, D., Angeli, A., Carta, F., Monti, S.M., De Simone, G., Alterio, V.

(2020) Chem Commun (Camb) 56: 8297-8300

• PubMed: 32573627 
• DOI: https://doi.org/10.1039/d0cc02857f
• Primary Citation of Related Structures:  
  6YQT, 6YQU


• PubMed Abstract: 
  

  2-Mercaptobenzoxazole is a widely used organic scaffold in medicinal chemistry. By means of kinetic and structural studies, we demonstrate that this molecule can effectively be used to inhibit hCAs showing a peculiar binding mode. The results reported here can pave the way for the development of selective CA inhibitors.

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Organizational Affiliation: 

Neurofarba Department, Section of Pharmaceutical and Nutriceutical Sciences, Università degli Studi di Firenze, 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 29.89 kDa 
• Atom Count: 2,351 
• Modelled 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P9E (Subject of Investigation/LOI)	C [auth A], D [auth A]	2-sulfanylidene-3~{H}-1,3-benzoxazole-5-sulfonamide C7 H6 N2 O3 S2 SCMGHROIQYCXRC-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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.206 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.170 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.425	α = 90
b = 41.484	β = 104.28
c = 72.093	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Alterio, V., De Simone, G., Esposito, D.

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Funding Organization	Location	Grant Number
Italian Ministry of Education	Italy	MOLIM ONCOBRAIN LAB

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2020-08-05
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description