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 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    5FL4, 5FL6, 5FL5

  • 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, which, in turn, favors tumor growth and metastasis ...

    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

    Faculty of Biology, Department of Molecular Biology, University of Latvia , Jelgavas 1, LV-1004, Riga, Latvia.



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
UniProt & NIH Common Fund Data Resources
Find proteins for Q16790 (Homo sapiens)
Explore Q16790 
Go to UniProtKB:  Q16790
PHAROS:  Q16790
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9FK (Subject of Investigation/LOI)
Query on 9FK

Download Ideal Coordinates CCD File 
F [auth A], K [auth B], O [auth C], U [auth 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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A], L [auth B], P [auth C], V [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A], J [auth B], N [auth C], T [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], M [auth B], Q [auth C], R [auth C], S [auth C]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9FK BindingDB:  5FL4 Ki: 101 (nM) from 1 assay(s)
Binding MOAD:  5FL4 Ki: 101 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.29α = 90
b = 152.29β = 90
c = 172.13γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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