1J4R | pdb_00001j4r

FK506 BINDING PROTEIN COMPLEXED WITH FKB-001

• PDB DOI: https://doi.org/10.2210/pdb1J4R/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.249 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

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: 11735566 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

Bristol-Myers Squibb Pharmaceutical Research Institute, P.O. Box 5100, Wallingford, Connecticut 06492-7660, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.67 kDa 
• Atom Count: 2,804 
• Modelled Residue Count: 321 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FK506-BINDING PROTEIN	A, B, C [auth D]	107	Homo sapiens	Mutation(s): 0  EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62942 (Homo sapiens) Explore P62942  Go to UniProtKB:  P62942
PHAROS:  P62942 GTEx:  ENSG00000088832

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
001	D [auth A], G [auth B], I [auth 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
SO4	F [auth B], H [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.249 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56	α = 90
b = 56	β = 90
c = 78.4	γ = 120

Software Package:

Software Name	Purpose
X-GEN	data scaling
X-GEN	data reduction
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description