8BOE | pdb_00008boe

Human Carbonic Anhydrase I in complex with (S)-4-(3-(1-(6-nitropyridin-2-yl)pyrrolidin-3-yl)thioureido)benzenesulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.172 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.153 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8BOE

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

First-in-Class Dual Hybrid Carbonic Anhydrase Inhibitors and Transient Receptor Potential Vanilloid 1 Agonists Revert Oxaliplatin-Induced Neuropathy.

Angeli, A.Micheli, L.Carta, F.Ferraroni, M.Pirali, T.Fernandez Carvajal, A.Ferrer Montiel, A.Di Cesare Mannelli, L.Ghelardini, C.Supuran, C.T.

(2023) J Med Chem 66: 1616-1633

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01911
  • Primary Citation Related Structures: 
    8BJX, 8BOE

  • PubMed Abstract: 

    Here, we report for the first time a series of compounds potentially useful for the management of oxaliplatin-induced neuropathy (OINP) able to modulate the human Carbonic Anhydrases (hCAs) as well as the Transient Receptor Potential Vanilloid 1 (TRPV1). All compounds showed effective in vitro inhibition activity toward the main hCAs involved in such a pathology, whereas selected items reported moderate agonism of TRPV1. X-ray crystallographic experiments assessed the binding modes of the two enantiomers ( R )- 37a and ( S )- 37b within the hCA II cleft. Although the tails assumed diverse orientations, no appreciable effects were observed for their hCA II affinity. Similarly, the activity of ( R )- 39a and ( S )- 39b on TRPV1 was not influenced by the stereocenters. In vivo evaluation of the most promising derivatives ( R )- 12a , ( R )- 37a , and the two enantiomers ( R )- 39a , ( S )- 39b revealed antihypersensitivity effects in a mouse model of OINP with potent and persistent effect up to 75 min after administration.


  • Organizational Affiliation
    • NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence, via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.

Macromolecule Content 

  • Total Structure Weight: 29.87 kDa 
  • Atom Count: 2,357 
  • Modeled Residue Count: 257 
  • Deposited Residue Count: 260 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2A [auth AAA]260Homo 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
Expand
Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
QKO BindingDB:  8BOE Ki: 6.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.172 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.153 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.58α = 90
b = 41.83β = 104.74
c = 72.78γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
RESOLVEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Database references
  • Version 1.2: 2026-03-04
    Changes: Refinement description, Structure summary