1J4R

FK506 BINDING PROTEIN COMPLEXED WITH FKB-001

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 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


  • 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 th ...

    [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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FK506-BINDING PROTEIN
A, B, D
107Homo sapiensMutation(s): 0 
Gene Names: FKBP1A (FKBP1, FKBP12)
EC: 5.2.1.8
Find proteins for P62942 (Homo sapiens)
Go to Gene View: FKBP1A
Go to UniProtKB:  P62942
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
001
Query on 001
Download SDF File 
Download 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
FKB-001
C35 H42 F2 N2 O6
NBYCDVVSYOMFMS-VMPREFPWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
001Ki: 19 nM BINDINGMOAD
1Ki: 19 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 56.000α = 90.00
b = 56.000β = 90.00
c = 78.400γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-GENdata scaling
AMoREphasing
X-GENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description