4WUP | pdb_00004wup

Crystal structure of human carbonic anhydrase isozyme I with 4-[(2-Hydroxyethyl)thio]benzenesulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.232 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Intrinsic thermodynamics of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamide binding to carbonic anhydrases by isothermal titration calorimetry.

Zubriene, A.Smirnoviene, J.Smirnov, A.Morkunaite, V.Michailoviene, V.Jachno, J.Juozapaitiene, V.Norvaisas, P.Manakova, E.Grazulis, S.Matulis, D.

(2015) Biophys Chem 205: 51-65

  • DOI: https://doi.org/10.1016/j.bpc.2015.05.009
  • Primary Citation Related Structures: 
    4WR7, 4WUP, 4WUQ, 4WW6, 4WW8

  • PubMed Abstract: 

    Para substituted tetrafluorobenzenesulfonamides bind to carbonic anhydrases (CAs) extremely tightly and exhibit some of the strongest known protein-small ligand interactions, reaching an intrinsic affinity of 2 pM as determined by displacement isothermal titration calorimetry (ITC). The enthalpy and entropy of binding to five CA isoforms were measured by ITC in two buffers of different protonation enthalpies. The pKa values of compound sulfonamide groups were measured potentiometrically and spectrophotometrically, and enthalpies of protonation were measured by ITC in order to evaluate the proton linkage contributions to the observed binding thermodynamics. Intrinsic means the affinity of a sulfonamide anion for the Zn bound water form of CAs. Fluorination of the benzene ring significantly enhanced the observed affinities as it increased the fraction of deprotonated ligand while having little impact on intrinsic affinities. Intrinsic enthalpy contributions to the binding affinity were dominant over entropy and were more exothermic for CA I than for other CA isoforms. Thermodynamic measurements together with the X-ray crystallographic structures of protein-ligand complexes enabled analysis of structure-activity relationships in this enzyme ligand system.


  • Organizational Affiliation
    • Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania. Electronic address: astzu@ibt.lt.

Macromolecule Content 

  • Total Structure Weight: 58.43 kDa 
  • Atom Count: 4,517 
  • Modeled Residue Count: 513 
  • Deposited Residue Count: 520 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carbonic anhydrase 1
A, B
260Homo sapiensMutation(s): 0 
Gene Names: CA1
EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00915 (Homo sapiens)
Explore P00915 
Go to UniProtKB:  P00915
PHAROS:  P00915
GTEx:  ENSG00000133742 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00915
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3UF

Query on 3UF



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
4-[(2-hydroxyethyl)sulfanyl]benzenesulfonamide
C8 H11 N O3 S2
LTXDVFFEVZJDGT-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
H [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
E [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
ACT BindingDB:  4WUP Ki: 1.08e+4 (nM) from 1 assay(s)
3UF BindingDB:  4WUP Kd: min: 200, max: 790 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.332α = 90
b = 71.284β = 90
c = 120.719γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
SCALAdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Data collection
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description