PDBsum entry 4knm

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protein ligands metals Protein-protein interface(s) links
Lyase/lyase inhibitor PDB id
Protein chains
259 a.a.
E1E ×2
_ZN ×2
Waters ×338
PDB id:
Name: Lyase/lyase inhibitor
Title: Crystal structure of human carbonic anhydrase isozyme xiii w chloro-4-{[(4,6-dimethylpyrimidin-2-yl) sulfanyl]acetyl}benzenesulfonamide
Structure: Carbonic anhydrase 13. Chain: a, b. Synonym: carbonate dehydratase xiii, carbonic anhydrase xii xiii. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ca13. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.90Å     R-factor:   0.184     R-free:   0.235
Authors: A.Smirnov,E.Manakova,S.Grazulis
Key ref: E.Čapkauskaitė et al. (2013). Benzenesulfonamides with pyrimidine moiety as inhibitors of human carbonic anhydrases I, II, VI, VII, XII, and XIII. Bioorg Med Chem, 21, 6937-6947. PubMed id: 24103428 DOI: 10.1016/j.bmc.2013.09.029
10-May-13     Release date:   06-Nov-13    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q8N1Q1  (CAH13_HUMAN) -  Carbonic anhydrase 13
262 a.a.
259 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Carbonate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
= CO(2)
+ H(2)O
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     myelin sheath   2 terms 
  Biological process     small molecule metabolic process   3 terms 
  Biochemical function     lyase activity     4 terms  


    Added reference    
DOI no: 10.1016/j.bmc.2013.09.029 Bioorg Med Chem 21:6937-6947 (2013)
PubMed id: 24103428  
Benzenesulfonamides with pyrimidine moiety as inhibitors of human carbonic anhydrases I, II, VI, VII, XII, and XIII.
E.Čapkauskaitė, A.Zubrienė, A.Smirnov, J.Torresan, M.Kišonaitė, J.Kazokaitė, J.Gylytė, V.Michailovienė, V.Jogaitė, E.Manakova, S.Gražulis, S.Tumkevičius, D.Matulis.
Two groups of benzenesulfonamide derivatives, bearing pyrimidine moieties, were designed and synthesized as inhibitors of carbonic anhydrases (CA). Their binding affinities to six recombinant human CA isoforms I, II, VI, VII, XII, and XIII were determined by the thermal shift assay (TSA). The binding of several inhibitors was measured by isothermal titration calorimetry (ITC). Direct demonstration of compound inhibition was achieved by determining the inhibition constant by stopped-flow CO2 hydration assay. The most potent compounds demonstrated selectivity towards isoform I and affinities of 0.5nM. The crystal structures of selected compounds in complex with CA II, XII, and XIII were determined to atomic resolution. Compounds described here were compared with previously published pyrimidinebenzenesulfonamides.(1) Systematic structure-activity analysis of 40 compound interactions with six isoforms yields clues for the design of compounds with greater affinities and selectivities towards target CA isoforms.