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: 29950.63 
• Atom Count: 2136 
• Residue Count: 260 
• Unique protein chains: 1

3M67

Crystal structure of human carbonic anhydrase isozyme II with 2-chloro-5-[(6,7-dihydro-1H-[1,4]dioxino[2,3-f]benzimidazol-2-ylsulfanyl)acetyl]benzenesulfonamide

• DOI: 10.2210/pdb3M67/pdb

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


• Deposited: 2010-03-15 Released: 2010-11-03 
• Deposition Author(s): Grazulis, S., Manakova, E., Golovenko, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.228 
• R-Value Work: 0.176 

Literature

Indapamide-like benzenesulfonamides as inhibitors of carbonic anhydrases I, II, VII, and XIII

Capkauskaite, E., Baranauskiene, L., Golovenko, D., Manakova, E., Grazulis, S., Tumkevicius, S., Matulis, D.

(2010) Bioorg.Med.Chem. 18: 7357-7364

• PubMed: 20926301 
• DOI: 10.1016/j.bmc.2010.09.016
• Primary Citation of Related Structures:  
  3MYQ, 3M96


• PubMed Abstract: 
  

A series of novel 2-chloro-5-[(1-benzimidazolyl- and 2-benzimidazolylsulfanyl)acetyl]benzene-sulfonamides were designed and synthesized. Their binding to recombinant human carbonic anhydrase (hCA) isozymes I, II, VII, and XIII was determined by isothermal titration calorimetry and thermal shift assay. The designed S-alkylated benzimidazole derivatives exhibited stronger binding than the indapamide-like N-alkylated benzimidazoles, with the K(d) reaching about 50-100 nM with drug-targeted hCAs VII and XIII. The cocrystal structures of selected compounds with hCA II were determined by X-ray crystallography, and structural features of the binding event were revealed.

---

Organizational Affiliation: 

Laboratory of Biothermodynamics and Drug Design, Institute of Biotechnology, 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
E36	A	2-chloro-5-[(6,7-dihydro-1H-[1,4]dioxino[2,3-f]benzimidazol-2-ylsulfanyl)acetyl]benzenesulfonamide C17 H14 Cl N3 O5 S2 CPDWGRXCTGPNOE-UHFFFAOYSA-N
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
E36	Kd: 20 - 1800 nM (100) BINDINGDB
E36	Kd: 180 nM BINDINGMOAD
E36	Kd: 180 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.228 
• R-Value Work: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 41.972	α = 90.00
b = 41.007	β = 104.43
c = 71.681	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-03-15 
• Released Date: 2010-11-03 
• Deposition Author(s): Grazulis, S., Manakova, E., Golovenko, D.

Revision History 

• Version 1.0: 2010-11-03
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance