9R30 | pdb_00009r30

Three dimensional structure of human carbonic anhydrase IX in complex with sulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.206 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Di- meta -Substituted Fluorinated Benzenesulfonamides as Potent and Selective Anticancer Inhibitors of Carbonic Anhydrase IX and XII.

Vaskevicius, A.Zvirblis, M.Kurtenoka, M.Leitans, J.Manakova, E.Paketuryte-Latve, V.Kvietkauskaite, A.Kazaks, A.Eimonta, V.Cerepenkaite, K.Kazokaite-Adomaitiene, J.Mickeviciu̅te, A.Juozapaitiene, V.Tars, K.Grazulis, S.Matuliene, J.Dudutiene, V.Shubin, K.Matulis, D.Zubriene, A.

(2025) J Med Chem 68: 18389-18406

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01142
  • Primary Citation of Related Structures:  
    9F2N, 9F2O, 9F30, 9F3G, 9R0L, 9R0U, 9R30, 9R31

  • PubMed Abstract: 

    The development of selective drug candidate molecules for cancer-related carbonic anhydrase isozymes IX and XII is challenging due to high homology binding sites among 12 catalytically active isozymes. Starting from the trifluorinated benzenesulfonamide with cyclooctylamino substituent at the meta position, we designed and synthesized di- meta -substituted fluorinated benzenesulfonamides with up to 10-fold affinity improvement for CAIX, resulting in low picomolar binders. The resulting CAIX-targeting compounds showed up to 1000-fold selectivity over off-target CA isozymes. The crystal structures of CAIX and CAXII complexes with synthesized compounds revealed detailed insights into protein-ligand interactions and adopted complex conformation. The potential of compounds with reduced off-target effects as possible anticancer drugs is supported by this study.


  • Organizational Affiliation
    • Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase
A, B, C, D
256Homo sapiensMutation(s): 2 
Gene Names: CA9
EC: 4.2.1.1
UniProt
Find proteins for A0A2R9BYT1 (Pan paniscus)
Explore A0A2R9BYT1 
Go to UniProtKB:  A0A2R9BYT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2R9BYT1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JC2 (Subject of Investigation/LOI)
Query on A1JC2

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
2,6-bis(fluoranyl)-4-methylsulfonyl-3,5-bis[(4-oxidanylcyclohexyl)amino]benzenesulfonamide
C19 H29 F2 N3 O6 S2
NWLSRXMQTUZBGB-ROTMJFINSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.206 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.585α = 90
b = 152.585β = 90
c = 172.572γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European Union5.2.1.1.i.0/2/24/I/CFLA/001

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Database references