PDBsum entry 1j4r

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Isomerase PDB id
Protein chains
107 a.a. *
001 ×3
SO4 ×2
Waters ×148
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Fk506 binding protein complexed with fkb-001
Structure: Fk506-binding protein. Chain: a, b, d. Synonym: fkbp, fkbp-1, peptidyl-prolyl cis-trans isomerase, rotamase, immunophilin fkbp12. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
1.80Å     R-factor:   0.205     R-free:   0.249
Authors: S.Sheriff
Key ref: G.M.Dubowchik et al. (2001). 2-Aryl-2,2-difluoroacetamide FKBP12 ligands: synthesis and X-ray structural studies. Org Lett, 3, 3987-3990. PubMed id: 11735566
29-Oct-01     Release date:   19-Dec-01    
Go to PROCHECK summary

Protein chains
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   10 terms 
  Biological process     chaperone-mediated protein folding   33 terms 
  Biochemical function     ion channel binding     16 terms  


    Added reference    
Org Lett 3:3987-3990 (2001)
PubMed id: 11735566  
2-Aryl-2,2-difluoroacetamide FKBP12 ligands: synthesis and X-ray structural studies.
G.M.Dubowchik, V.M.Vrudhula, B.Dasgupta, J.Ditta, T.Chen, S.Sheriff, K.Sipman, M.Witmer, J.Tredup, D.M.Vyas, T.A.Verdoorn, S.Bollini, A.Vinitsky.
[structure: see text] 2-Aryl-2,2-difluoroacetamido-proline and pipecolate esters are high affinity FKBP12 ligands whose rotamase inhibitory activity is comparable to that seen for the corresponding ketoamides. X-ray structural studies suggest that the fluorine atoms participate in discrete interactions with the Phe36 phenyl ring and the Tyr26 hydroxyl group, with the latter resembling a moderate-to-weak hydrogen bond.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21455526 Z.Chen, J.Zhu, H.Xie, S.Li, Y.Wu, and Y.Gong (2011).
A cascade process for the synthesis of gem-difluoromethylene compounds.
  Org Biomol Chem, 9, 3878-3885.  
17541991 C.H.Röhrig, C.Loch, J.Y.Guan, G.Siegal, and M.Overhand (2007).
Fragment-Based Synthesis and SAR of Modified FKBP Ligands: Influence of Different Linking on Binding Affinity.
  ChemMedChem, 2, 1054-1070.  
17387719 I.Nakanishi, D.G.Fedorov, and K.Kitaura (2007).
Molecular recognition mechanism of FK506 binding protein: an all-electron fragment molecular orbital study.
  Proteins, 68, 145-158.  
16302169 X.J.Wang, and F.A.Etzkorn (2006).
Peptidyl-prolyl isomerase inhibitors.
  Biopolymers, 84, 125-146.  
15122639 J.A.Olsen, D.W.Banner, P.Seiler, B.Wagner, T.Tschopp, U.Obst-Sander, M.Kansy, K.Müller, and F.Diederich (2004).
Fluorine interactions at the thrombin active site: protein backbone fragments H-C(alpha)-C=O comprise a favorable C-F environment and interactions of C-F with electrophiles.
  Chembiochem, 5, 666-675.  
12579579 J.H.Lin, A.L.Perryman, J.R.Schames, and J.A.McCammon (2003).
The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme.
  Biopolymers, 68, 47-62.  
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