Crystal structure of human carbonic anhydrase isozyme II with 4-{[N-(6-chloro-5-formyl-2-methylthiopyrimidin-4-yl)amino]methyl}benzenesulfonamide

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.168 

Starting Model: experimental
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4-[N-(Substituted 4-pyrimidinyl)amino]benzenesulfonamides as inhibitors of carbonic anhydrase isozymes I, II, VII, and XIII

Sudzius, J.Baranauskiene, L.Golovenko, D.Matuliene, J.Michailoviene, V.Torresan, J.Jachno, J.Sukackaite, R.Manakova, E.Grazulis, S.Tumkevicius, S.Matulis, D.

(2010) Bioorg Med Chem 18: 7413-7421

  • DOI: https://doi.org/10.1016/j.bmc.2010.09.011
  • Primary Citation of Related Structures:  
    3M3X, 3M40, 3M5E, 3MHI, 3MHL, 3MHM, 3MHO

  • PubMed Abstract: 

    A series of 4-[N-(substituted 4-pyrimidinyl)amino]benzenesulfonamides were designed and synthesised. Their binding potencies as inhibitors of selected recombinant human carbonic anhydrase (hCA) isozymes I, II, VII, and XIII were measured using isothermal titration calorimetry and the thermal shift assay. To determine the structural features of inhibitor binding, the crystal structures of several compounds in complex with hCA II were determined. Several compounds exhibited selectivity towards isozymes I, II, and XIII, and some were potent inhibitors of hCA VII.

  • Organizational Affiliation

    Department of Organic Chemistry, Faculty of Chemistry, Vilnius University, Naugarduko 24, LT-03225 Vilnius, Lithuania.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
GTEx:  ENSG00000104267 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on JDR

Download Ideal Coordinates CCD File 
D [auth A]4-({[6-chloro-5-formyl-2-(methylsulfanyl)pyrimidin-4-yl]amino}methyl)benzenesulfonamide
C13 H13 Cl N4 O3 S2
Query on DMS

Download Ideal Coordinates CCD File 
C2 H6 O S
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Binding Affinity Annotations 
IDSourceBinding Affinity
JDR BindingDB:  3M5E Kd: min: 24, max: 43 (nM) from 2 assay(s)
PDBBind:  3M5E Kd: 43 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.423α = 90
b = 41.486β = 104.49
c = 72.434γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
Omodel 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: 2010-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description