PDBsum entry 1i9l

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Lyase PDB id
Protein chain
258 a.a. *
INV ×2
Waters ×99
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Carbonic anhydrase ii (f131v) complexed with 4- (aminosulfonyl)-n-[(4-fluorophenyl)methyl]-benzamide
Structure: Carbonic anhydrase ii. Chain: a. Synonym: carbonate dehydratase ii. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
1.93Å     R-factor:   0.223     R-free:   0.280
Authors: C.-Y.Kim,P.P.Chandra,A.Jain,D.W.Christianson
Key ref: C.Y.Kim et al. (2001). Fluoroaromatic-fluoroaromatic interactions between inhibitors bound in the crystal lattice of human carbonic anhydrase II. J Am Chem Soc, 123, 9620-9627. PubMed id: 11572683 DOI: 10.1021/ja011034p
20-Mar-01     Release date:   28-Mar-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00918  (CAH2_HUMAN) -  Carbonic anhydrase 2
260 a.a.
258 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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     extracellular space   11 terms 
  Biological process     angiotensin-mediated signaling pathway   22 terms 
  Biochemical function     protein binding     5 terms  


    Added reference    
DOI no: 10.1021/ja011034p J Am Chem Soc 123:9620-9627 (2001)
PubMed id: 11572683  
Fluoroaromatic-fluoroaromatic interactions between inhibitors bound in the crystal lattice of human carbonic anhydrase II.
C.Y.Kim, P.P.Chandra, A.Jain, D.W.Christianson.
Intermolecular interactions of eleven different fluoroaromatic inhibitors are probed within the scaffolding of the crystal lattice of Phe-131-->Val carbonic anhydrase II. The degree and pattern of fluorine substitution on the inhibitor benzyl ring modulate its size, shape, and electronic character. In turn, these properties affect the geometry of intermolecular interactions between the fluoroaromatic rings of two different inhibitor molecules bound in the crystal lattice, as determined by X-ray crystallography. Depending on the degree and pattern of fluorine substitution, we observe a face-to-face (aromatic-aromatic) interaction, an atom-to-face (carbonyl-aromatic) interaction, or no interaction at all. These interaction geometries are analyzed with regard to van der Waals, electrostatic, and possible charge-transfer effects. For the aromatic-aromatic interactions investigated in this study, with aromatic ring quadrupoles specifically "tuned" by the degree and pattern of fluorination, the structural results suggest that London forces and charge-transfer complexation dominate over weakly polar electrostatic interactions in the association of aromatic ring pairs.

Literature references that cite this PDB file's key reference

  PubMed id Reference
18335973 V.M.Krishnamurthy, G.K.Kaufman, A.R.Urbach, I.Gitlin, K.L.Gudiksen, D.B.Weibel, and G.M.Whitesides (2008).
Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding.
  Chem Rev, 108, 946.  
17910057 A.Amini, P.J.Shrimpton, S.H.Muggleton, and M.J.Sternberg (2007).
A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming.
  Proteins, 69, 823-831.  
17334823 K.H.Kim (2007).
Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers?
  J Comput Aided Mol Des, 21, 63-86.  
17901324 K.Müller, C.Faeh, and F.Diederich (2007).
Fluorine in pharmaceuticals: looking beyond intuition.
  Science, 317, 1881-1886.
PDB codes: 2v3h 2v3o
16506782 K.M.Jude, A.L.Banerjee, M.K.Haldar, S.Manokaran, B.Roy, S.Mallik, D.K.Srivastava, and D.W.Christianson (2006).
Ultrahigh resolution crystal structures of human carbonic anhydrases I and II complexed with "two-prong" inhibitors reveal the molecular basis of high affinity.
  J Am Chem Soc, 128, 3011-3018.
PDB codes: 2foq 2fos 2fou 2fov 2foy
15526325 M.Kontoyianni, G.S.Sokol, and L.M.McClellan (2005).
Evaluation of library ranking efficacy in virtual screening.
  J Comput Chem, 26, 11-22.  
15122635 H.J.Böhm, D.Banner, S.Bendels, M.Kansy, B.Kuhn, K.Müller, U.Obst-Sander, and M.Stahl (2004).
Fluorine in medicinal chemistry.
  Chembiochem, 5, 637-643.  
12944268 E.Metwally, H.A.Ismail, J.S.Davison, and R.Mathison (2003).
A tree-based algorithm for determining the effects of solvation on the structure of salivary gland tripeptide NH3+-D-PHE-D-GLU-GLY-COO-.
  Biophys J, 85, 1503-1511.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.