Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 30031.68 
• Atom Count: 2262 
• Residue Count: 260 
• Unique protein chains: 1

3M2N

Crystal structure of human carbonic anhydrase isozyme II with 4-{2-[N-(6-chloro-5-nitropyrimidin-4-yl)amino]ethyl}benzenesulfonamide

• DOI: 10.2210/pdb3M2N/pdb

• Classification: LYASE/LYASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2010-03-08 Released: 2011-02-16 
• Deposition Author(s): Grazulis, S., Manakova, E., Golovenko, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.203 
• R-Value Work: 0.155 

Literature

Design of [(2-pyrimidinylthio)acetyl]benzenesulfonamides as inhibitors of human carbonic anhydrases.

Capkauskaite, E., Zubriene, A., Baranauskiene, L., Tamulaitiene, G., Manakova, E., Kairys, V., Grazulis, S., Tumkevicius, S., Matulis, D.

(2012) Eur.J.Med.Chem. 51: 259-270

• PubMed: 22440859 
• DOI: 10.1016/j.ejmech.2012.02.050
• Primary Citation of Related Structures:  
  3SBI, 3SBH, 3SAX, 3SAP, 3S9T, 3S8X


• PubMed Abstract: 
  

A series of [(2-pyrimidinylthio)acetyl]benzenesulfonamides were designed and synthesized. Their binding affinities as inhibitors of several recombinant human carbonic anhydrase (CA) isozymes were determined by isothermal titration calorimetry (ITC) and thermal shift assay (TSA). A group of compounds containing a chlorine atom in the benzenesulfonamide ring were found to exhibit higher selectivity but lower binding affinity toward tested CAs. The crystal structures of selected compounds in complex with CA II were determined to atomic resolution. Docking studies were performed to compare the binding modes of experimentally determined crystallographic structures with computational prediction of the pyrimidine derivative binding to CA II. Several compounds bound to select CAs with single-digit nanomolar affinities and could be used as leads for inhibitor development toward a select CA isozyme.

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Organizational Affiliation: 

Vilnius University, Institute of Biotechnology, Department of Biothermodynamics and Drug Design, Graičiūno 8, Vilnius LT-02241, Lithuania.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens) Go to Gene View: CA2 Go to UniProtKB:  P00918

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
J74	A	4-{2-[(6-chloro-5-nitropyrimidin-4-yl)amino]ethyl}benzenesulfonamide C12 H12 Cl N5 O4 S XPZIHQXLSDNLNB-UHFFFAOYSA-N
BCN	A	BICINE C6 H13 N O4 FSVCELGFZIQNCK-UHFFFAOYSA-N
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.203 
• R-Value Work: 0.155 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 42.041	α = 90.00
b = 41.253	β = 104.74
c = 71.858	γ = 90.00

Software Package:

Software Name	Purpose
MAR345	data collection
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-03-08 
• Released Date: 2011-02-16 
• Deposition Author(s): Grazulis, S., Manakova, E., Golovenko, D.

Revision History 

• Version 1.0: 2011-02-16
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2012-05-16
  Type: Database references
• Version 1.3: 2017-11-08
  Type: Refinement description