8EXC | pdb_00008exc

Human Carbonic Anhydrase II bound tert-butyl (3-(4-(3-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)propoxy)butoxy)propyl)carbamate

• PDB DOI: https://doi.org/10.2210/pdb8EXC/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-25 Released: 2023-02-22 
• Deposition Author(s): Kohlbrand, A.J., O'Herin, C.B.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Development of Human Carbonic Anhydrase II Heterobifunctional Degraders.

O'Herin, C.B., Moriuchi, Y.W., Bemis, T.A., Kohlbrand, A.J., Burkart, M.D., Cohen, S.M.

(2023) J Med Chem 

• PubMed: 36735827 
• DOI: https://doi.org/10.1021/acs.jmedchem.2c01843
• Primary Citation Related Structures: 
  8EMU, 8EXC, 8EXG, 8EYL


• PubMed Abstract: 
  

  Human carbonic anhydrase II (hCAII) is a metalloenzyme essential to critical physiological processes in the body. hCA inhibitors are used clinically for the treatment of indications ranging from glaucoma to epilepsy. Targeted protein degraders have emerged as a promising means of inducing the degradation of disease-implicated proteins by using the endogenous quality control mechanisms of a cell. Here, a series of heterobifunctional degrader candidates targeting hCAII were developed from a simple aryl sulfonamide fragment. Degrader candidates were functionalized to produce either cereblon E3 ubiquitin ligase (CRBN) recruiting proteolysis targeting chimeras (PROTACs) or adamantyl-based hydrophobic tags (HyTs). Screens in HEK293 cells identified two PROTAC small-molecule degraders of hCA. Optimization of linker length and composition yielded a degrader with sub-nanomolar potency and sustained depletion of hCAII over prolonged treatments. Mechanistic studies suggest that this optimized degrader depletes hCAII through the same mechanism as previously reported CRBN-recruiting heterobifunctional degraders.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, La Jolla, California 92093, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.32 kDa 
• Atom Count: 2,350 
• Modeled Residue Count: 257 
• 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): 0  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
X2U (Subject of Investigation/LOI)	B [auth A]	N-(3-{4-[3-({2-[(3R)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}amino)propoxy]butoxy}propyl)-4-sulfamoylbenzamide C30 H37 N5 O9 S RBECNOZCCFLMDH-XMMPIXPASA-N
MBO	D [auth A]	MERCURIBENZOIC ACID C7 H5 Hg O2 FVFZSVRSDNUCGG-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.986	α = 90
b = 41.222	β = 104.211
c = 71.874	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
APEX	data reduction
APEX	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-22 
Deposition Author(s): Kohlbrand, A.J., O'Herin, C.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI149444

Revision History  

• Version 1.0: 2023-02-22
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description