3HKU

Human carbonic anhydrase II in complex with topiramate

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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • 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 inhibito ...

    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.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 2A260Homo sapiensMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TOR
Query on TOR
Download CCD File 
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		 Ligand Interaction
ZN
Query on ZN
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TORKi:  450   nM  BindingDB
TORKi:  430   nM  BindingDB
TORKi:  7700   nM  BindingDB
TORIC50:  5   nM  BindingDB
TORKi:  10   nM  BindingDB
TORKi:  9600   nM  BindingDB
TORKi:  10000   nM  BindingDB
TORKi :  5   nM  PDBBind
TORKi:  500   nM  BindingDB
TORKi:  9   nM  BindingDB
TORKi:  10.300000190734863   nM  BindingDB
TORKd:  290   nM  BindingDB
TORIC50:  2100   nM  BindingDB
TORKd:  13.800000190734863   nM  BindingDB
TORKi:  5   nM  BindingDB
TORKi:  300   nM  BindingDB
TORKi:  5000   nM  BindingDB
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 = 42.264α = 90
b = 41.426β = 104.59
c = 72.44γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

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