8FR2

Carbonic Anhydrase IX-mimic in complex with the alkyl urea compound 3h

• PDB DOI: https://doi.org/10.2210/pdb8FR2/pdb

• Classification: METAL BINDING PROTEIN, Lyase
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-01-06 Released: 2023-02-01 
• Deposition Author(s): Combs, J.C., McKenna, R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 0.179 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

Starting Model: experimental

Literature

New Insights into Conformationally Restricted Carbonic Anhydrase Inhibitors.

Combs, J., Bozdag, M., Cravey, L.D., Kota, A., McKenna, R., Angeli, A., Carta, F., Supuran, C.T.

(2023) Molecules 28

• PubMed: 36677947 
• DOI: https://doi.org/10.3390/molecules28020890
• Primary Citation of Related Structures:  
  8FQX, 8FQY, 8FQZ, 8FR1, 8FR2, 8FR4


• PubMed Abstract: 
  

  This paper reports an investigation into the impact of pyridyl functional groups in conjunction with hydroxide-substituted benzenesulfonamides on the inhibition of human carbonic anhydrase (CA; EC 4.2.1.1) enzymes. These compounds were tested in vitro of CA II and CA IX, two physiologically important CA isoforms. The most potent inhibitory molecules against CA IX, 3g , 3h , and 3k , were studied to understand their binding modes via X-ray crystallography in adduct with CA II and CA IX-mimic. This research further adds to the field of CA inhibitors to better understand ligand selectivity between isoforms found in humans.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.43 kDa 
• Atom Count: 2,421 
• Modelled Residue Count: 257 
• Deposited Residue Count: 257 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	257	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
N8A (Subject of Investigation/LOI)	C [auth A]	4-hydroxy-3-({[2-(pyridin-2-yl)ethyl]carbamoyl}amino)benzene-1-sulfonamide C14 H16 N4 O4 S BTQJGTGBPQIYNN-UHFFFAOYSA-N
GOL	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: 1.31 Å
• R-Value Free: 0.179 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.879	α = 90
b = 41.193	β = 103.84
c = 71.976	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-01 
Deposition Author(s): Combs, J.C., McKenna, R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-02-01
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection