8RNS | pdb_00008rns

Human Carbonic Anhydrase XII mimic in complex with biguanide derivative inhibitor 1-carbamimidamido-N-[(4 sulfamoylphenyl)methyl]methanimidamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 
    0.161 (Depositor), 0.165 (DCC) 
  • R-Value Work: 
    0.141 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.143 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

X-ray crystallographic and kinetic studies of biguanide containing aryl sulfonamides as carbonic anhydrase inhibitors.

Baroni, C.Bozdag, M.Renzi, G.De Luca, V.Capasso, C.Bazzicalupi, C.Selleri, S.Ferraroni, M.Carta, F.Supuran, C.T.

(2025) RSC Med Chem 16: 1633-1640

  • DOI: https://doi.org/10.1039/d4md01018c
  • Primary Citation Related Structures: 
    8RNS, 8ROU, 8ROW, 9H0V

  • PubMed Abstract: 

    Here, we report a small series of dual-targeting compounds that combine the prototypical carbonic anhydrase (CA) zinc-binding sulfonamide moiety with the biguanide group of metformin, an emerging anticancer drug. The compounds reported similar in vitro inhibition profiles on a panel of physiologically relevant human (h)CAs, with marked selectivity for the cancer related IX and XII isoforms. The binding modes of representative inhibitors 5b and 5c within the active site of the hCA isoforms II and XII-mimic were assessed by X-ray crystallography, thus allowing us to clarify molecular features that may be useful for the design of more specific and potent inhibitors. For instance, we identified a mutation in the hCA XII-mimic which was found responsible for the selectivity of the ligands toward the tumor associated isoform. Interestingly, in the hCA II/5c complex, a second inhibitor molecule was bound to the catalytic cleft, probably affecting the inhibition properties of the canonical zinc-bound inhibitor.


  • Organizational Affiliation
    • Department of Chemistry "Ugo Schiff", University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino FI Italy marta.ferraroni@unifi.it.

Macromolecule Content 

  • Total Structure Weight: 29.57 kDa 
  • Atom Count: 2,443 
  • 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): 9 
Gene Names: CA2
EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (PDB Primary Data)
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free:  0.161 (Depositor), 0.165 (DCC) 
  • R-Value Work:  0.141 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.143 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.98α = 90
b = 41.33β = 103.87
c = 71.81γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2026-02-11
    Changes: Database references