4RIU

A Carbonic Anhydrase IX Mimic in Complex with a Saccharin-Based Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4RIU/pdb

• Classification: Lyase/Lyase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-10-07 Released: 2015-02-04 
• Deposition Author(s): Mahon, B.P., McKenna, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.176 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 

Starting Model: experimental

Literature

Saccharin: A lead compound for structure-based drug design of carbonic anhydrase IX inhibitors.

Mahon, B.P., Hendon, A.M., Driscoll, J.M., Rankin, G.M., Poulsen, S.A., Supuran, C.T., McKenna, R.

(2015) Bioorg Med Chem 23: 849-854

• PubMed: 25614109 
• DOI: https://doi.org/10.1016/j.bmc.2014.12.030
• Primary Citation of Related Structures:  
  4RIU, 4RIV


• PubMed Abstract: 
  

  Carbonic anhydrase IX (CA IX) is a key modulator of aggressive tumor behavior and a prognostic marker and target for several cancers. Saccharin (SAC) based compounds may provide an avenue to overcome CA isoform specificity, as they display both nanomolar affinity and preferential binding, for CA IX compared to CA II (>50-fold for SAC and >1000-fold when SAC is conjugated to a carbohydrate moiety). The X-ray crystal structures of SAC and a SAC-carbohydrate conjugate bound to a CA IX-mimic are presented and compared to CA II. The structures provide substantial new insight into the mechanism of SAC selective CA isoform inhibition.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, FL 32610, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.98 kDa 
• Atom Count: 2,340 
• Modelled Residue Count: 258 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 7  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3QR	F [auth A]	[1-(1,1-dioxido-3-oxo-2,3-dihydro-1,2-benzothiazol-6-yl)-1H-1,2,3-triazol-4-yl]methyl alpha-L-idopyranoside C16 H18 N4 O9 S CUFOYUJLNJPOJR-HSMHQDCBSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.176 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.996	α = 90
b = 41.215	β = 103.83
c = 71.834	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-04 
Deposition Author(s): Mahon, B.P., McKenna, R.

Revision History  

• Version 1.0: 2015-02-04
  Type: Initial release
  
• Version 1.1: 2015-02-25
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description