Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 29834.80 
• Atom Count: 2110 
• Residue Count: 259 
• Unique protein chains: 1

3IBU

The crystal structure of the human carbonic anhydrase II in complex with an aliphatic sulfamate inhibitor

• DOI: 10.2210/pdb3IBU/pdb

• Classification: LYASE/LYASE INHIBITOR
• Organism(s): Homo sapiens


• Deposited: 2009-07-17 Released: 2009-09-22 
• Deposition Author(s): Alterio, V., De Simone, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.215 
• R-Value Work: 0.200 

Literature

Carbonic anhydrase inhibitors. Comparison of aliphatic sulfamate/bis-sulfamate adducts with isozymes II and IX as a platform for designing tight-binding, more isoform-selective inhibitors

Vitale, R.M., Alterio, V., Innocenti, A., Winum, J.-Y., Monti, S.M., De Simone, G., Supuran, C.T.

(2009) J.Med.Chem. 52: 5990-5998

• PubMed: 19731956 
• DOI: 10.1021/jm900641r
• Primary Citation of Related Structures:  
  3IBN, 3IBL, 3IBI


• PubMed Abstract: 
  

Two approaches were used to design inhibitors of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1): the tail and the ring approaches. Aliphatic sulfamates constitute a class of CA inhibitors (CAIs) that cannot be classified in either one of these categories. We report here the detailed inhibition profile of four such compounds against isoforms CAs I-XIV, the first crystallographic structures of these compounds in adduct with isoform II, and molecular modeling studies for their interaction with hCA IX. Aliphatic monosulfamates/bis-sulfamates were nanomolar inhibitors of hCAs II, IX, and XII, unlike aromatic/heterocyclic sulfonamides that promiscuously inhibit most CA isozymes with low nanomolar affinity. The bis-sulfamates incorporating 8 or 10 carbon atoms showed higher affinity for the tumor-associated hCA IX compared to hCA II, whereas the opposite was true for the monosulfamates. The explanation for their interaction with CA active site furnishes insights for obtaining compounds with increased affinity/selectivity for various isozymes.

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Organizational Affiliation: 

Istituto di Chimica Biomolecolare-CNR, Pozzuoli, Italy.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Carbonic anhydrase 2	A	259	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
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
O48	A	decyl sulfamate n-decyl sulfamate C10 H23 N O3 S JBKMRMOTMJVNML-UHFFFAOYSA-N
HGB	A	4-(HYDROXYMERCURY)BENZOIC ACID C7 H6 Hg O3 WMHRYLDWLOGHSG-UHFFFAOYSA-M

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
O48	Ki: 0.7 nM (100) BINDINGDB
CL	Ki: 200000000 nM (100) BINDINGDB
O48	Ki: 0.7 nM BINDINGMOAD
O48	Ki: 0.7 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.215 
• R-Value Work: 0.200 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 42.070	α = 90.00
b = 41.410	β = 104.29
c = 71.970	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
CNS	refinement
CNS	phasing
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-07-17 
• Released Date: 2009-09-22 
• Deposition Author(s): Alterio, V., De Simone, G.

Revision History 

• Version 1.0: 2009-09-22
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2011-08-24
  Type: Atomic model, Database references, Structure summary