4Q6E | pdb_00004q6e

Crystal structure of human carbonic anhydrase isozyme II with 4-{[3-(3,5-Dimethyl-1H-pyrazol-1-yl)-3-oxopropyl]amino}benzene-1-sulfonamide

• PDB DOI: https://doi.org/10.2210/pdb4Q6E/pdb

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


• Deposited: 2014-04-22 Released: 2014-11-26 
• Deposition Author(s): Smirnov, A., Manakova, E., Grazulis, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 
  0.158 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.130 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Starting Model: experimental

Literature

4-Amino-substituted Benzenesulfonamides as Inhibitors of Human Carbonic Anhydrases.

Rutkauskas, K., Zubriene, A., Tumosiene, I., Kantminiene, K., Kazemekaite, M., Smirnov, A., Kazokaite, J., Morkunaite, V., Capkauskaite, E., Manakova, E., Grazulis, S., Beresnevicius, Z.J., Matulis, D.

(2014) Molecules 19: 17356-17380

• PubMed: 25353386 
• DOI: https://doi.org/10.3390/molecules191117356
• Primary Citation of Related Structures:  
  4Q6D, 4Q6E


• PubMed Abstract: 
  

  A series of N-aryl-β-alanine derivatives and diazobenzenesulfonamides containing aliphatic rings were designed, synthesized, and their binding to carbonic anhydrases (CA) I, II, VI, VII, XII, and XIII was studied by the fluorescent thermal shift assay and isothermal titration calorimetry. The results showed that 4-substituted diazobenzenesulfonamides were more potent CA binders than N-aryl-β-alanine derivatives. Most of the N-aryl-β-alanine derivatives showed better affinity for CA II while diazobenzenesulfonamides possessed nanomolar affinities towards CA I isozyme. X-ray crystallographic structures showed the modes of binding of both compound groups.

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Organizational Affiliation: 
• Department of Organic Chemistry, Kaunas University of Technology, Kaunas LT-50254, Lithuania. [e-mail].
Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania. [e-mail].
Department of Organic Chemistry, Kaunas University of Technology, Kaunas LT-50254, Lithuania. [e-mail].
Department of Physical and Inorganic Chemistry, Kaunas University of Technology, Kaunas LT-50254, Lithuania. [e-mail].
Institute of Biochemistry, Vilnius University, Mokslininkų 12, Vilnius LT-08862, Lithuania. [e-mail].
Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania. [e-mail].
Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania. [e-mail].
Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania. [e-mail].
Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania. [e-mail].
Department of Protein-DNA Interactions, Vilnius University Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania. [e-mail].
Department of Protein-DNA Interactions, Vilnius University Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania. [e-mail].
Department of Organic Chemistry, Kaunas University of Technology, Kaunas LT-50254, Lithuania. [e-mail].
Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania. [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 kDa 
• Atom Count: 2,575 
• 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  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KR5	F [auth A]	4-{[3-(3,5-dimethyl-1H-pyrazol-1-yl)-3-oxopropyl]amino}benzenesulfonamide C14 H18 N4 O3 S SQGUOOCGLKRFBU-UHFFFAOYSA-N
BCN	C [auth A]	BICINE C6 H13 N O4 FSVCELGFZIQNCK-UHFFFAOYSA-N
DMS	D [auth A], 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: 1.12 Å
• R-Value Free:  0.158 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.130 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.237	α = 90
b = 41.241	β = 104.3
c = 72.189	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Smirnov, A., Manakova, E., Grazulis, S.

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Advisory, Data collection
• Version 1.2: 2023-09-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description