Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
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: 30206.56 
• Atom Count: 2203 
• Residue Count: 260 
• Unique protein chains: 1

3SBH

Crystal structure of human carbonic anhydrase isozyme II with 4-{[(4,6-dimethyl-2-pyrimidinyl)sulfanyl]acetyl}benzenesulfonamide

• DOI: 10.2210/pdb3SBH/pdb

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


• Deposited: 2011-06-05 Released: 2012-04-11 
• Deposition Author(s): Grazulis, S., Manakova, E., Tamulaitiene, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.228 
• R-Value Work: 0.172 

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, 3SAX, 3SAP, 3S9T, 3S8X, 3M2N


• 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
E65	A	4-{[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetyl}benzenesulfonamide C14 H15 N3 O3 S2 HSMLEDGQPDVPFW-UHFFFAOYSA-N
BCN	A	BICINE C6 H13 N O4 FSVCELGFZIQNCK-UHFFFAOYSA-N
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MES	A	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
E65	Kd: 33 - 52 nM (100) BINDINGDB
E65	Kd: 33 nM BINDINGMOAD
E65	Kd: 52 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.228 
• R-Value Work: 0.172 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 42.093	α = 90.00
b = 41.090	β = 104.17
c = 71.839	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
MOSFLM	data reduction
REFMAC	refinement
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-05 
• Released Date: 2012-04-11 
• Deposition Author(s): Grazulis, S., Manakova, E., Tamulaitiene, G.

Revision History 

• Version 1.0: 2012-04-11
  Type: Initial release
• Version 1.1: 2012-05-16
  Type: Database references
• Version 1.2: 2017-09-27
  Type: Advisory, Data collection, Refinement description