6RJJ

Human Carbonic Anhydrase II in complex with fluorinated benzenesulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.123 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase II.

Glockner, S.Ngo, K.Wagner, B.Heine, A.Klebe, G.

(2020) Biomolecules 10

  • DOI: https://doi.org/10.3390/biom10040509
  • Primary Citation of Related Structures:  
    6RH4, 6RIT, 6RJJ, 6RKN, 6RL9, 6RNP, 6ROB, 6ROE, 6RQI, 6RRG, 6RRI, 6RS5, 6RSZ, 6S9G, 6SD7

  • PubMed Abstract: 

    The fluorination of lead-like compounds is a common tool in medicinal chemistry to alter molecular properties in various ways and with different goals. We herein present a detailed study of the binding of fluorinated benzenesulfonamides to human Carbonic Anhydrase II by complementing macromolecular X-ray crystallographic observations with thermodynamic and kinetic data collected with the novel method of kinITC. Our findings comprise so far unknown alternative binding modes in the crystalline state for some of the investigated compounds as well as complex thermodynamic and kinetic structure-activity relationships. They suggest that fluorination of the benzenesulfonamide core is especially advantageous in one position with respect to the kinetic signatures of binding and that a higher degree of fluorination does not necessarily provide for a higher affinity or more favorable kinetic binding profiles. Lastly, we propose a relationship between the kinetics of binding and ligand acidity based on a small set of compounds with similar substitution patterns.


  • Organizational Affiliation

    Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2265Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
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
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BE7
Query on BE7

Download Ideal Coordinates CCD File 
D [auth A](4-CARBOXYPHENYL)(CHLORO)MERCURY
C7 H5 Cl Hg O2
YFZOUMNUDGGHIW-UHFFFAOYSA-M
HG
Query on HG

Download Ideal Coordinates CCD File 
C [auth A]MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
K5W (Subject of Investigation/LOI)
Query on K5W

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
2,3-bis(fluoranyl)benzenesulfonamide
C6 H5 F2 N O2 S
DWBWMAAYLWUXQK-UHFFFAOYSA-N
GLC
Query on GLC

Download Ideal Coordinates CCD File 
H [auth A]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
BGC
Query on BGC

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E [auth A]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.123 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.391α = 90
b = 41.678β = 104.56
c = 72.628γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description, Structure summary