Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 29.83 kDa 
• Atom Count: 2473 
• Residue Count: 258 
• 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
• Mutation(s): No 


• 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:  
  3IBI, 3IBU, 3IBL, 3IBN


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	259	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
NIH Common Fund Data Resources
PHAROS  P00918 GTEx  ENSG00000104267

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HGB	A	4-(HYDROXYMERCURY)BENZOIC ACID C7 H6 Hg O3 WMHRYLDWLOGHSG-UHFFFAOYSA-M
O48	A	decyl sulfamate C10 H23 N O3 S JBKMRMOTMJVNML-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
O48	Ki :  0.699999988079071   nM  PDBBind
O48	Ki:  0.699999988079071   nM  Binding MOAD
O48	Ki:  0.699999988079071   nM  BindingDB

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 = 42.07	α = 90
b = 41.41	β = 104.29
c = 71.97	γ = 90

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-08-24
  Changes: Atomic model, Database references, Structure summary