3HKT | pdb_00003hkt

Human carbonic anhydrase II in complex with alpha-D-Glucopyranosyl-(1->4)-1-thio-beta-D-glucopyranosylsulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 
    0.248 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3HKT

This is version 2.1 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: https://doi.org/10.1021/jm900914e
  • Primary Citation 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.


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

Macromolecule Content 

  • Total Structure Weight: 29.76 kDa 
  • Atom Count: 2,240 
  • Modeled Residue Count: 257 
  • Deposited Residue Count: 260 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
PHAROS:  P00918
GTEx:  ENSG00000104267 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-galactopyranose-(1-4)-(1S)-1,5-anhydro-1-sulfamoyl-D-galactitol
B
2N/AN/A
Glycosylation Resources
GlyTouCan: G46053DQ
GlyCosmos: G46053DQ

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free:  0.248 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.347α = 90
b = 41.671β = 104.92
c = 72.488γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-03-20
    Changes: Data collection, Database references, Structure summary