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: 29.69 kDa 
• Atom Count: 2426 
• Modelled Residue Count: 257 
• Deposited Residue Count: 260 
• Unique protein chains: 1

3HKU

Human carbonic anhydrase II in complex with topiramate

• DOI: 10.2210/pdb3HKU/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-25 Released: 2009-10-13 
• Deposition Author(s): Paul, B., Poulsen, S.-A., Hofmann, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.198 
• R-Value Work: 0.152 
• R-Value Observed: 0.155 

Literature

S-glycosyl primary sulfonamides--a new structural class for selective inhibition of cancer-associated carbonic anhydrases.

Lopez, M., Paul, B., Hofmann, A., Morizzi, J., Wu, Q.K., Charman, S.A., Innocenti, A., Vullo, D., Supuran, C.T., Poulsen, S.A.

(2009) J Med Chem 52: 6421-6432

• PubMed: 19827837 
• DOI: 10.1021/jm900914e
• Primary Citation of Related Structures:  
  3HKN, 3HKQ, 3HKT, 3HKU


• PubMed Abstract: 
  

In this paper, we present a new class of carbonic anhydrase (CA) inhibitor that was designed to selectively target the extracellular domains of the cancer-relevant CA isozymes. The aromatic moiety of the classical zinc binding sulfonamide CA inhibitors is absent from these compounds and instead they incorporate a hydrophilic mono- or disaccharide fragment directly attached to the sulfonamide group to give S-glycosyl primary sulfonamides (1-10). The inhibition properties of these compounds at the physiologically abundant human CA isozymes I and II and cancer-associated IX and XII were determined, and all compounds had moderate potency with K(i)s in the micromolar range. We present the crystal structures of anomeric sulfonamides 4, 7, and 10 and the sugar sulfamate drug topiramate in complex with human recombinant CA II. From these structures, we have obtained valuable insights into ligand-protein interactions of these novel carbohydrate-based sulfonamides with CA.

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Organizational Affiliation: 

Eskitis Institute for Cell and Molecular Therapies, Griffith University, Nathan, Queensland 4111, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TOR (Subject of Investigation/LOI)	C [auth A]	[(3aS,5aR,8aR,8bS)-2,2,7,7-tetramethyltetrahydro-3aH-bis[1,3]dioxolo[4,5-b:4',5'-d]pyran-3a-yl]methyl sulfamate C12 H21 N O8 S KJADKKWYZYXHBB-XBWDGYHZSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TOR	BindingDB:  3HKU	Ki: min: 5, max: 1.00e+4 (nM) from 12 assay(s)
		Kd: min: 13.8, max: 290 (nM) from 2 assay(s)
		IC50: min: 5, max: 2100 (nM) from 2 assay(s)
	PDBBind:  3HKU	Ki: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.198 
• R-Value Work: 0.152 
• R-Value Observed: 0.155 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.264	α = 90
b = 41.426	β = 104.59
c = 72.44	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2009-05-25 
• Released Date: 2009-10-13 
Deposition Author(s): Paul, B., Poulsen, S.-A., Hofmann, A.

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-12-25
  Changes: Database references