8EM3

Carbonic Anhydrase II in complex with the diaryl urea molecule J2

• PDB DOI: https://doi.org/10.2210/pdb8EM3/pdb

• Classification: METAL BINDING PROTEIN, Lyase/Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-26 Released: 2023-09-27 
• Deposition Author(s): Combs, J., McKenna, R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.184 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 

Literature

Prospective Diaryl urea: Prevent growth of breast cancer cells by inhibition and down-regulation of Carbonic Anhydrase IX.

Debnath, J., Keshamasetthy, D., Combs, J., Leon, K., McKenna, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.68 kDa 
• Atom Count: 2,275 
• Modelled 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WLE (Subject of Investigation/LOI)	B [auth A]	4-[(3-methoxyphenyl)carbamamido]benzene-1-sulfonamide C14 H15 N3 O4 S POERGDGPHIWSKB-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.184 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.564	α = 90
b = 41.601	β = 104.39
c = 72.466	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-27 
Deposition Author(s): Combs, J., McKenna, R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-09-27
  Type: Initial release