6FE1

Three dimensional structure of human carbonic anhydrase IX in complex with benzenesulfonamide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report



Literature

Novel fluorinated carbonic anhydrase IX inhibitors reduce hypoxia-induced acidification and clonogenic survival of cancer cells.

Kazokaite, J.Niemans, R.Dudutiene, V.Becker, H.M.Leitans, J.Zubriene, A.Baranauskiene, L.Gondi, G.Zeidler, R.Matuliene, J.Tars, K.Yaromina, A.Lambin, P.Dubois, L.J.Matulis, D.

(2018) Oncotarget 9: 26800-26816

  • DOI: 10.18632/oncotarget.25508
  • Primary Citation of Related Structures:  
    6G98, 6G9U, 6FE0, 6FE2, 6FE1

  • PubMed Abstract: 
  • Human carbonic anhydrase (CA) IX has emerged as a promising anticancer target and a diagnostic biomarker for solid hypoxic tumors. Novel fluorinated CA IX inhibitors exhibited up to 50 pM affinity towards the recombinant human CA IX, selectivity over ...

    Human carbonic anhydrase (CA) IX has emerged as a promising anticancer target and a diagnostic biomarker for solid hypoxic tumors. Novel fluorinated CA IX inhibitors exhibited up to 50 pM affinity towards the recombinant human CA IX, selectivity over other CAs, and direct binding to Zn(II) in the active site of CA IX inducing novel conformational changes as determined by X-ray crystallography. Mass spectrometric gas-analysis confirmed the CA IX-based mechanism of the inhibitors in a CRISPR/Cas9-mediated CA IX knockout in HeLa cells. Hypoxia-induced extracellular acidification was significantly reduced in HeLa, H460, MDA-MB-231, and A549 cells exposed to the compounds, with the IC 50 values up to 1.29 nM. A decreased clonogenic survival was observed when hypoxic H460 3D spheroids were incubated with our lead compound. These novel compounds are therefore promising agents for CA IX-specific therapy.


    Organizational Affiliation

    Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 9A, B, C, D257Homo sapiensMutation(s): 1 
Gene Names: CA9G250MN
EC: 4.2.1.1
Find proteins for Q16790 (Homo sapiens)
Explore Q16790 
Go to UniProtKB:  Q16790
NIH Common Fund Data Resources
PHAROS  Q16790
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V14
Query on V14

Download CCD File 
A, B, C, D
3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide
C16 H23 F3 N2 O5 S2
HFJJAVOBUVMVFQ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
V14Kd:  0.05000000074505806   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.02α = 90
b = 152.02β = 90
c = 172.21γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2017-12-28 
  • Released Date: 2018-07-04 
  • Deposition Author(s): Leitans, J., Tars, K.

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release