4Q07

Crystal structure of chimeric carbonic anhydrase IX with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery and characterization of novel selective inhibitors of carbonic anhydrase IX.

Dudutiene, V.Matuliene, J.Smirnov, A.Timm, D.D.Zubriene, A.Baranauskiene, L.Morkunaite, V.Smirnoviene, J.Michailoviene, V.Juozapaitiene, V.Mickeviciute, A.Kazokaite, J.Baksyte, S.Kasiliauskaite, A.Jachno, J.Revuckiene, J.Kisonaite, M.Pilipuityte, V.Ivanauskaite, E.Milinaviciute, G.Smirnovas, V.Petrikaite, V.Kairys, V.Petrauskas, V.Norvaisas, P.Linge, D.Gibieza, P.Capkauskaite, E.Zaksauskas, A.Kazlauskas, E.Manakova, E.Grazulis, S.Ladbury, J.E.Matulis, D.

(2014) J Med Chem 57: 9435-9446

  • DOI: 10.1021/jm501003k
  • Primary Citation of Related Structures:  
    4Q0L, 4Q06, 4Q07, 4Q08, 4Q09, 4PYX, 4PYY, 4PZH

  • PubMed Abstract: 
  • Human carbonic anhydrase IX (CA IX) is highly expressed in tumor tissues, and its selective inhibition provides a potential target for the treatment of numerous cancers. Development of potent, highly selective inhibitors against this target remains a ...

    Human carbonic anhydrase IX (CA IX) is highly expressed in tumor tissues, and its selective inhibition provides a potential target for the treatment of numerous cancers. Development of potent, highly selective inhibitors against this target remains an unmet need in anticancer therapeutics. A series of fluorinated benzenesulfonamides with substituents on the benzene ring was designed and synthesized. Several of these exhibited a highly potent and selective inhibition profile against CA IX. Three fluorine atoms significantly increased the affinity by withdrawing electrons and lowering the pKa of the benzenesulfonamide group. The bulky ortho substituents, such as cyclooctyl or even cyclododecyl groups, fit into the hydrophobic pocket in the active site of CA IX but not CA II, as shown by the compound's co-crystal structure with chimeric CA IX. The strongest inhibitor of recombinant human CA IX's catalytic domain in human cells achieved an affinity of 50 pM. However, the high affinity diminished the selectivity. The most selective compound for CA IX exhibited 10 nM affinity. The compound that showed the best balance between affinity and selectivity bound with 1 nM affinity. The inhibitors described in this work provide the basis for novel anticancer therapeutics targeting CA IX.


    Organizational Affiliation

    Department of Biothermodynamics and Drug Design, Institute of Biotechnology, ‡Department of Bioinformatics, Institute of Biotechnology, §Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University , V. A. Graičiu̅no 8, Vilnius LT-02241, Lithuania.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 2A260Homo sapiensMutation(s): 6 
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V14
Query on V14

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

Download CCD File 
A
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-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 %)
V14Kd:  4.800000190734863   nM  BindingDB
V14Kd:  5   nM  Binding MOAD
V14Kd:  8.699999809265137   nM  BindingDB
V14Kd:  29   nM  BindingDB
V14Kd:  59   nM  BindingDB
V14Kd:  60   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.131 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.931α = 90
b = 41.214β = 104.21
c = 72.066γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Data collection