1J4R

FK506 BINDING PROTEIN COMPLEXED WITH FKB-001


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

2-Aryl-2,2-difluoroacetamide FKBP12 ligands: synthesis and X-ray structural studies.

Dubowchik, G.M.Vrudhula, V.M.Dasgupta, B.Ditta, J.Chen, T.Sheriff, S.Sipman, K.Witmer, M.Tredup, J.Vyas, D.M.Verdoorn, T.A.Bollini, S.Vinitsky, A.

(2001) Org Lett 3: 3987-3990

  • DOI: 10.1021/ol0166909
  • Primary Citation of Related Structures:  
    1J4R

  • PubMed Abstract: 
  • [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 fl ...

    [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.


    Organizational Affiliation

    Bristol-Myers Squibb Pharmaceutical Research Institute, P.O. Box 5100, Wallingford, Connecticut 06492-7660, USA. gene.dubowchik@bms.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FK506-BINDING PROTEIN ABD107Homo sapiensMutation(s): 0 
Gene Names: FKBP1AFKBP1FKBP12
EC: 5.2.1.8
Find proteins for P62942 (Homo sapiens)
Explore P62942 
Go to UniProtKB:  P62942
NIH Common Fund Data Resources
PHAROS:  P62942
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
001
Query on 001

Download Ideal Coordinates CCD File 
A, B, D
1-[2,2-DIFLUORO-2-(3,4,5-TRIMETHOXY-PHENYL)-ACETYL]-PIPERIDINE-2-CARBOXYLIC ACID 4-PHENYL-1-(3-PYRIDIN-3-YL-PROPYL)-BUTYL ESTER
C35 H42 F2 N2 O6
NBYCDVVSYOMFMS-VMPREFPWSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
001Ki:  19   nM  Binding MOAD
1Ki :  19   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56α = 90
b = 56β = 90
c = 78.4γ = 120
Software Package:
Software NamePurpose
X-GENdata scaling
X-GENdata reduction
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2001-10-29 
  • Released Date: 2001-12-19 
  • Deposition Author(s): Sheriff, S.

Revision History 

  • Version 1.0: 2001-12-19
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description