7BI5

Human CA II in complex with benzyl alcohol

• PDB DOI: https://doi.org/10.2210/pdb7BI5/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-01-12 Released: 2021-03-17 
• Deposition Author(s): Alterio, V., De Simone, G.
• Funding Organization(s): Italian Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.194 
• R-Value Work: 0.170 

Starting Model: experimental

Literature

Benzyl alcohol inhibits carbonic anhydrases by anchoring to the zinc coordinated water molecule.

De Simone, G., Bua, S., Supuran, C.T., Alterio, V.

(2021) Biochem Biophys Res Commun 548: 217-221

• PubMed: 33647799 
• DOI: https://doi.org/10.1016/j.bbrc.2021.02.067
• Primary Citation of Related Structures:  
  7BI5


• PubMed Abstract: 
  

  Up to date alcohols have been scarcely investigated as carbonic anhydrase (CA) inhibitors. To get more insights into the CA inhibition properties of this class of molecules, in this paper, by means of inhibition assays and X-ray crystallographic studies we report a detailed characterization of the CA inhibition properties and the binding mode to human CA II of benzyl alcohol. Results show that, although possessing a very simple scaffold, this molecule acts as a micromolar CA II inhibitor, which anchors to the enzyme active site by means of an H-bond interaction with the zinc bound solvent molecule. Taken together our results clearly indicate primary alcohols as a class of CA inhibitors that deserve to be more investigated.

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Organizational Affiliation: 

Istituto di Biostrutture e Bioimmagini-CNR, Naples, Italy. Electronic address: [e-mail].

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: 29.46 kDa 
• Atom Count: 2,260 
• Modelled Residue Count: 256 
• 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
010 (Subject of Investigation/LOI)	C [auth A]	phenylmethanol C7 H8 O WVDDGKGOMKODPV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.194 
• R-Value Work: 0.170 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.324	α = 90
b = 41.333	β = 104.3
c = 71.86	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Alterio, V., De Simone, G.

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Funding Organization	Location	Grant Number
Italian Ministry of Education	Italy	201744BNST

Revision History  

• Version 1.0: 2021-03-17
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description