9GFW | pdb_00009gfw

HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH 4-methylphenyl-boronic acid at pH 7.4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 
    0.162 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.141 (Depositor) 
  • R-Value Observed: 
    0.142 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Exploring the binding mode of phenyl and vinyl boronic acids to human carbonic anhydrases.

Esposito, D.Monti, S.M.Supuran, C.T.Winum, J.Y.De Simone, G.Alterio, V.

(2024) Int J Biol Macromol 282: 136873-136873

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.136873
  • Primary Citation Related Structures: 
    9GFV, 9GFW, 9GFX

  • PubMed Abstract: 

    Boronic acids are an interesting but still poorly studied class of carbonic anhydrase inhibitors. Previous investigations proved that derivatives incorporating aromatic, arylalkyl, and arylalkenyl moieties are low micromolar to millimolar inhibitors for several α- and β-CAs involved in pathologic states. Here we report a high-resolution X-ray study on two classes of boronic acids (phenyl and vinyl) in complex with hCA II. Our results unambiguously clarify the binding mode of these molecules to the human carbonic anhydrase active site, which occurs through their tetrahedral anionic form, regardless of the nature of the organic scaffold. Data here presented contribute to the understanding of the inhibition mechanism of boronic acids that can be fruitfully used for the rational design of novel and effective isozyme-specific carbonic anhydrase inhibitors.


  • Organizational Affiliation
    • Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche (IBB-CNR), Via Pietro Castellino, 111, 80131 Naples, Italy.

Macromolecule Content 

  • Total Structure Weight: 30 kDa 
  • Atom Count: 2,343 
  • Modeled Residue Count: 258 
  • Deposited Residue Count: 260 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MBO

Query on MBO



Download:Ideal Coordinates CCD File
F [auth A]MERCURIBENZOIC ACID
C7 H5 Hg O2
FVFZSVRSDNUCGG-UHFFFAOYSA-N
A1IKU
(Subject of Investigation/LOI)

Query on A1IKU



Download:Ideal Coordinates CCD File
C [auth A](4-methylphenyl)-tris(oxidanyl)boron
C7 H10 B O3
BBVYZRUHVNLQBZ-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
E [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free:  0.162 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.141 (Depositor) 
  • R-Value Observed: 0.142 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.195α = 90
b = 41.443β = 104.43
c = 72.084γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
Omodel building
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian National Research Council (CNR)ItalyJoint Bilateral Agreements CNR/CINVESTAV
Ministero dell Universita e della RicercaItalyP2022EPH87

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references