PDBsum entry 1j4i

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protein ligands links
Isomerase PDB id
Protein chain
107 a.a. *
Waters ×119
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure analysis of the fkbp12 complexed with 000308 small molecule
Structure: Fkbp12. Chain: a. Synonym: fk506-binding protein. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
1.80Å     R-factor:   0.185     R-free:   0.209
Authors: P.Li,Y.Ding,L.Wang,B.Wu,C.Shu,S.Li,B.Shen,Z.Rao
Key ref: F.Sun et al. (2003). Design and structure-based study of new potential FKBP12 inhibitors. Biophys J, 85, 3194-3201. PubMed id: 14581219
30-Sep-01     Release date:   03-Jun-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P62942  (FKB1A_HUMAN) -  Peptidyl-prolyl cis-trans isomerase FKBP1A
108 a.a.
107 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Peptidylprolyl isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidylproline (omega=180) = peptidylproline (omega=0)
Peptidylproline (omega=180)
= peptidylproline (omega=0)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   7 terms 
  Biological process     chaperone-mediated protein folding   26 terms 
  Biochemical function     ion channel binding     14 terms  


    Added reference    
Biophys J 85:3194-3201 (2003)
PubMed id: 14581219  
Design and structure-based study of new potential FKBP12 inhibitors.
F.Sun, P.Li, Y.Ding, L.Wang, M.Bartlam, C.Shu, B.Shen, H.Jiang, S.Li, Z.Rao.
Based on the structure of FKBP12 complexed with FK506 or rapamycin, with computer-aided design, two neurotrophic ligands, (3R)-4-(p-Toluenesulfonyl)-1,4-thiazane-3-carboxylic acid-L-Leucine ethyl ester and (3R)-4-(p-Toluenesulfonyl)-1,4-thiazane-3-carboxylic acid-L-phenylalanine benzyl ester, were designed and synthesized. Fluorescence experiments were used to detect the binding affinity between FKBP12 and these two ligands. Complex structures of FKBP12 with these two ligands were obtained by x-ray crystallography. In comparing FKBP12-rapamycin complex and FKBP12-FK506 complex as well as FKBP12-GPI-1046 solution structure with these new complexes, significant volume and surface area effects and obvious contact changes were detected which are expected to cause their different binding energies-showing these two novel ligands will become more effective neuron regeneration drugs than GPI-1046, which is currently undergoing phase II clinical trail as a neurotrophic drug. Analysis of volume and surface area effects also gives a new clue for structure-based drug design.

Literature references that cite this PDB file's key reference

  PubMed id Reference
18004757 M.H.Cheng, R.D.Coalson, and M.Cascio (2008).
Molecular dynamics simulations of ethanol binding to the transmembrane domain of the glycine receptor: implications for the channel potentiation mechanism.
  Proteins, 71, 972-981.  
16838311 Y.Xu, and R.Wang (2006).
A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method.
  Proteins, 64, 1058-1068.  
16262683 N.Ramachandran, D.N.Larson, P.R.Stark, E.Hainsworth, and J.LaBaer (2005).
Emerging tools for real-time label-free detection of interactions on functional protein microarrays.
  FEBS J, 272, 5412-5425.  
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