Crystal structure of human carbonic anhydrase I in complex with the 3-(2,5-dimethylphenyl)-1-(2-hydroxy-5-sulfamoylphenyl)urea inhibitor

Experimental Data Snapshot

  • Resolution: 1.99 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

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Discovery of 4-Hydroxy-3-(3-(phenylureido)benzenesulfonamides as SLC-0111 Analogues for the Treatment of Hypoxic Tumors Overexpressing Carbonic Anhydrase IX.

Bozdag, M.Carta, F.Ceruso, M.Ferraroni, M.McDonald, P.C.Dedhar, S.Supuran, C.T.

(2018) J Med Chem 61: 6328-6338

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00770
  • Primary Citation of Related Structures:  
    6F3B, 6FAF, 6FAG

  • PubMed Abstract: 

    Herein we report the 2-aminophenol-4-sulfonamide 1 and its ureido derivatives 2-23 as inhibitors of the carbonic anhydrase (CA, EC enzymes as analogues of the hypoxic tumor phase II entering drug SLC-0111. This scaffold may determine preferential rotational isomers to selectively interact within the tumor-associated CAs. Most of the compounds indeed showed in vitro selective inhibition of the tumor associated CA isoforms IX and XII. The most potent derivative within the series was 11 ( K I s of 2.59 and 7.64 nM on hCA IX and XII, respectively), which shares the 4-fluorophenylureido tail with the clinical candidate. We investigated by means of X-ray crystallographic studies the binding modes of three selected compounds of this series to CA I. The evaluation of therapeutic efficacy of compound 11 in an orthotopic, syngeneic model of CA IX-positive breast cancer in vivo showed close matching antitumoral effects and tolerance with SLC-0111.

  • Organizational Affiliation

    University of Florence , Department of Chemistry "Ugo Schiff" , Via della Lastruccia 3 , 50019 Sesto Fiorentino ( Florence ), Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 1
A, B
261Homo sapiensMutation(s): 0 
Gene Names: CA1
EC: (PDB Primary Data), (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00915 (Homo sapiens)
Explore P00915 
Go to UniProtKB:  P00915
PHAROS:  P00915
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00915
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D3B (Subject of Investigation/LOI)
Query on D3B

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
C15 H17 N3 O4 S
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B]
C3 H8 O3
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
D3B Binding MOAD:  6FAF Ki: 306.1 (nM) from 1 assay(s)
BindingDB:  6FAF Ki: 306 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.99 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.803α = 90
b = 71.086β = 90
c = 120.554γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
MxCuBEdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release