8CDX

Human carbonic anhydrase I complexed with 4-(3-ethylureido)benzenesulfonamide

• PDB DOI: https://doi.org/10.2210/pdb8CDX/pdb

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


• Deposited: 2023-02-01 Released: 2024-02-21 
• Deposition Author(s): Angeli, A., Ferraroni, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.179 
• R-Value Work: 0.141 

Starting Model: experimental

Literature

Ureidobenzenesulfonamides as Selective Carbonic Anhydrase I, IX, and XII Inhibitors.

Denner, T.C., Angeli, A., Ferraroni, M., Supuran, C.T., Csuk, R.

(2023) Molecules 28

• PubMed: 38067512 
• DOI: https://doi.org/10.3390/molecules28237782
• Primary Citation of Related Structures:  
  8CDX, 8CDZ


• PubMed Abstract: 
  

  Sulfonamides remain an important class of drugs, especially because of their inhibitory effects on carbonic anhydrases. Herein, we have synthesized several sulfonamides and tested them for their inhibitory activity against carbonic anhydrases hCA I, hCA II, hCA IX, and hCA XII, respectively. Thereby, biphenyl- and benzylphenyl-substituted sulfonamides showed high selectivity against hCA IX and hCA XII; these enzymes are common targets in the treatment of hypoxic cancers, and noteworthy inhibitory activity was observed for several compounds toward hCA I that might be of interest for future applications to treat cerebral edema. Compound 3 (4-[3-(2-benzylphenyl)ureido]benzenesulfonamide) held an exceptionally low K _i value of 1.0 nM for hCA XII.

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Organizational Affiliation: 

Organic Chemistry, Martin-Luther University Halle-Wittenberg, Kurt-Mothes, Str. 2, D-06120 Halle (Saale), Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 58.43 kDa 
• Atom Count: 4,592 
• Modelled Residue Count: 514 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 1	A [auth AAA], B [auth BBB]	261	Homo sapiens	Mutation(s): 0  Gene Names: CA1 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00915 (Homo sapiens) Explore P00915  Go to UniProtKB:  P00915
PHAROS:  P00915 GTEx:  ENSG00000133742

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UE7 (Subject of Investigation/LOI)	D [auth AAA], F [auth BBB]	1-ethyl-3-(4-sulfamoylphenyl)urea C9 H13 N3 O3 S MMKFCCLMBRGOIK-UHFFFAOYSA-N
ZN	C [auth AAA], E [auth BBB]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.179 
• R-Value Work: 0.141 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.27	α = 90
b = 70.98	β = 90
c = 121.58	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): Angeli, A., Ferraroni, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release
  
• Version 1.1: 2024-09-04
  Changes: Database references