5FL4

Three dimensional structure of human carbonic anhydrase IX in complex with 5-(1-naphthalen-1-yl-1,2,3-triazol-4-yl)thiophene-2-sulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

An Efficient Expression and Crystallization System of the Cancer Asociated Carbonic Anhydrase Isoform Ix.

Leitans, J.Kazaks, A.Balode, A.Ivanova, J.Zalubovskis, R.Supuran, C.T.Tars, K.

(2015) J.Med.Chem. 58: 9004

  • DOI: 10.1021/acs.jmedchem.5b01343
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human carbonic anhydrase IX (CA IX) is overexpressed in a number of solid tumors and is considered to be a marker for cellular hypoxia that it is not produced in most normal tissues. CA IX contributes to the acidification of the extracellular matrix, ...

    Human carbonic anhydrase IX (CA IX) is overexpressed in a number of solid tumors and is considered to be a marker for cellular hypoxia that it is not produced in most normal tissues. CA IX contributes to the acidification of the extracellular matrix, which, in turn, favors tumor growth and metastasis. Therefore, CA IX is considered to be a promising anti-cancer drug target. However, the ability to specifically target CA IX is challenging due to the fact that the human genome encodes 15 different carbonic anhydrase isoforms that have a high degree of homology. Furthermore, structure-based drug design of CA IX inhibitors so far has been largely unsuccessful due to technical difficulties regarding the expression and crystallization of the enzyme. Currently, only one baculovirus-produced CA IX structure in complex with a nonspecific CA inhibitor, acetazolamide, is available in Protein Data Bank. We have developed an efficient system for the production of the catalytic domain of CA IX in methylotrophic yeast Pichia pastoris. The produced protein can be easily crystallized in the presence of inhibitors, as we have demonstrated for several 2-thiophene-sulfonamide compounds. We have also observed significant differences in the binding mode of chemically identical compounds to CA IX and CA II, which can be further exploited in the design of CA IX-specific inhibitors.


    Organizational Affiliation

    Biomedical Research and Study Center , Ratsupites 1, LV-1067, Riga, Latvia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBONIC ANHYDRASE 9
A, B, C, D
257Homo sapiensMutation(s): 1 
Gene Names: CA9 (G250, MN)
EC: 4.2.1.1
Find proteins for Q16790 (Homo sapiens)
Go to Gene View: CA9
Go to UniProtKB:  Q16790
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9FK
Query on 9FK

Download SDF File 
Download CCD File 
A, B, C, D
5-(1-naphthalen-1-yl-1,2,3-triazol-4-yl)thiophene-2-sulfonamide
C16 H12 N4 O2 S2
KNFVNHRBTIJTNM-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A, B, C
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.190 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 152.290α = 90.00
b = 152.290β = 90.00
c = 172.130γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-12-09
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Data collection
  • Version 1.3: 2019-01-30
    Type: Data collection, Experimental preparation
  • Version 1.4: 2019-02-06
    Type: Data collection, Experimental preparation