3N4B

Crystal structure of human carbonic anhydrase II in complex with a benzenesulfonamide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3N4B/pdb

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


• Deposited: 2010-05-21 Released: 2011-03-09 
• Deposition Author(s): Avvaru, B.S., Wagner, J., Robbins, A.H., McKenna, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.170 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 

Starting Model: experimental

Literature

Selective hydrophobic pocket binding observed within the carbonic anhydrase II active site accommodate different 4-substituted-ureido-benzenesulfonamides and correlate to inhibitor potency.

Pacchiano, F., Aggarwal, M., Avvaru, B.S., Robbins, A.H., Scozzafava, A., McKenna, R., Supuran, C.T.

(2010) Chem Commun (Camb) 46: 8371-8373

• PubMed: 20922253 
• DOI: https://doi.org/10.1039/c0cc02707c
• Primary Citation of Related Structures:  
  3MZC, 3N0N, 3N2P, 3N3J, 3N4B


• PubMed Abstract: 
  

  4-Substituted-ureido benzenesulfonamides showing inhibitory activity against carbonic anhydrase (CA, EC 4.2.1.1) II between 3.3-226 nM were crystallized in complex with the enzyme. Hydrophobic interactions between the scaffold of the inhibitors in different hydrophobic pockets of the enzyme were observed, explaining the diverse inhibitory range of these derivatives.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Box 100245, Gainesville, Florida 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: 29.76 kDa 
• Atom Count: 2,419 
• 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): 0  Gene Names: HCA2 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
WWZ	C [auth A]	4-{[(4-fluorophenyl)carbamoyl]amino}benzenesulfonamide C13 H12 F N3 O3 S YJQZNWPYLCNRLP-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
WWZ	BindingDB:  3N4B	Ki: min: 96, max: 960 (nM) from 2 assay(s)
	PDBBind:  3N4B	Ki: 96 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.170 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.465	α = 90
b = 41.414	β = 104.13
c = 72.037	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-09 
Deposition Author(s): Avvaru, B.S., Wagner, J., Robbins, A.H., McKenna, R.

Revision History  

• Version 1.0: 2011-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description