6G6T

Crystal structure of human carbonic anhydrase isozyme II with N-butyl-2,4-dichloro-5-sulfamoyl-benzamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.147 

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Literature

Design of two-tail compounds with rotationally fixed benzenesulfonamide ring as inhibitors of carbonic anhydrases.

Zaksauskas, A., Capkauskaite, E., Jezepcikas, L., Linkuviene, V., Kisonaite, M., Smirnov, A., Manakova, E., Grazulis, S., Matulis, D.

(2018) Eur J Med Chem 156: 61-78

  • DOI: 10.1016/j.ejmech.2018.06.059
  • Primary Citation of Related Structures:  
    6G5L, 6G5U, 6G6T, 6G7A

  • PubMed Abstract: 

    • Rational design of compounds that would bind specific pockets of the target proteins is a difficult task in drug design. The 12 isoforms of catalytically active human carbonic anhydrases (CAs) have highly similar active sites that make it difficult to design inhibitors selective for one or several CA isoforms ...

    Rational design of compounds that would bind specific pockets of the target proteins is a difficult task in drug design. The 12 isoforms of catalytically active human carbonic anhydrases (CAs) have highly similar active sites that make it difficult to design inhibitors selective for one or several CA isoforms. A series of CA inhibitors based on 2-chloro/bromo-benzenesulfonamide that is largely fixed in the CA active site together with one or two tails yielded compounds that were synthesized and evaluated as inhibitors of CA isoforms. Introduction of a second tail had significant influence on the binding affinity and two-tailed compounds in most cases provided high affinity and selectivity for CA IX and CA XIV. The contacts between several compounds and CA amino acids were determined by X-ray crystallography. Together with the intrinsic enthalpy and entropy of binding they provided the structure-thermodynamics correlations for this series of compounds with the insight how to rationally build compounds with desired CA isoform as a target.

    Organizational Affiliation: 

    Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania. Electronic address: matulis@ibt.lt.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 2A260Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ENN
Query on ENN
Download Ideal Coordinates CCD File 
E [auth A]~{N}-butyl-2,4-bis(chloranyl)-5-sulfamoyl-benzamide
C11 H14 Cl2 N2 O3 S
KRIUYRKSVUBELV-UHFFFAOYSA-N		 Ligand Interaction
BCN
Query on BCN
Download Ideal Coordinates CCD File 
D [auth A]BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
C [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ENN BindingDB:  6G6T Kd: min: 0.14, max: 20 (nM) from 3 assay(s)
Binding MOAD:  6G6T Kd: 0.16 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.147 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.057α = 90
b = 41.196β = 104.19
c = 72.094γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release