9F3G | pdb_00009f3g

Human carbonic anhydrase XII with 3-(cyclooctylamino)-2,6-difluoro-5-((4-hydroxybutyl)amino)-4-((3-hydroxypropyl)sulfonyl)benzenesulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 
    0.168 (Depositor), 0.173 (DCC) 
  • R-Value Work: 
    0.137 (Depositor), 0.149 (DCC) 
  • R-Value Observed: 
    0.140 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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 12
A, B, C, D
263Homo sapiensMutation(s): 0 
Gene Names: CA12
EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for O43570 (Homo sapiens)
Explore O43570 
Go to UniProtKB:  O43570
PHAROS:  O43570
GTEx:  ENSG00000074410 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43570
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H91 (Subject of Investigation/LOI)
Query on A1H91

Download Ideal Coordinates CCD File 
DA [auth D],
J [auth A],
Q [auth B],
V [auth C]
3-(cyclooctylamino)-2,6-bis(fluoranyl)-5-(4-oxidanylbutylamino)-4-[(~{E})-3-oxidanylprop-1-enyl]sulfonyl-benzenesulfonamide
C21 H35 F2 N3 O6 S2
DACKPNNKPOPNSA-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
CA [auth D],
I [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
R [auth C],
W [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
F [auth A]
G [auth A]
H [auth A]
AA [auth D],
BA [auth D],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
S [auth C],
T [auth C],
U [auth C],
X [auth D],
Y [auth D],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free:  0.168 (Depositor), 0.173 (DCC) 
  • R-Value Work:  0.137 (Depositor), 0.149 (DCC) 
  • R-Value Observed: 0.140 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.501α = 90
b = 74.116β = 108.83
c = 91.632γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
iNEXT-DiscoveryEuropean Union871037

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Database references
  • Version 1.2: 2025-09-24
    Changes: Database references