Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.96 kDa 
• Atom Count: 1825 
• Modelled Residue Count: 214 
• Deposited Residue Count: 214 
• Unique protein chains: 1

1BL4

FKBP MUTANT F36V COMPLEXED WITH REMODELED SYNTHETIC LIGAND

• DOI: 10.2210/pdb1BL4/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-07-23 Released: 1998-09-02 
• Deposition Author(s): Hatada, M.H., Clackson, T., Yang, W., Rozamus, L.W., Amara, J., Rollins, C.T., Stevenson, L.F., Magari, S.R., Wood, S.A., Courage, N.L., Lu, X., Cerasoli Junior, F., Gilman, M., Holt, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.230 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 

Literature

Redesigning an FKBP-ligand interface to generate chemical dimerizers with novel specificity.

Clackson, T., Yang, W., Rozamus, L.W., Hatada, M., Amara, J.F., Rollins, C.T., Stevenson, L.F., Magari, S.R., Wood, S.A., Courage, N.L., Lu, X., Cerasoli Jr., F., Gilman, M., Holt, D.A.

(1998) Proc Natl Acad Sci U S A 95: 10437-10442

• PubMed: 9724721 
• DOI: 10.1073/pnas.95.18.10437
• Primary Citation of Related Structures:  
  1BL4


• PubMed Abstract: 
  

FKBP ligand homodimers can be used to activate signaling events inside cells and animals that have been engineered to express fusions between appropriate signaling domains and FKBP. However, use of these dimerizers in vivo is potentially limited by ligand binding to endogenous FKBP. We have designed ligands that bind specifically to a mutated FKBP over the wild-type protein by remodeling an FKBP-ligand interface to introduce a specificity binding pocket. A compound bearing an ethyl substituent in place of a carbonyl group exhibited sub-nanomolar affinity and 1,000-fold selectivity for a mutant FKBP with a compensating truncation of a phenylalanine residue. Structural and functional analysis of the new pocket showed that recognition is surprisingly relaxed, with the modified ligand only partially filling the engineered cavity. We incorporated the specificity pocket into a fusion protein containing FKBP and the intracellular domain of the Fas receptor. Cells expressing this modified chimeric protein potently underwent apoptosis in response to AP1903, a homodimer of the modified ligand, both in culture and when implanted into mice. Remodeled dimerizers such as AP1903 are ideal reagents for controlling the activities of cells that have been modified by gene therapy procedures, without interference from endogenous FKBP.

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Organizational Affiliation: 

ARIAD Gene Therapeutics, Inc., 26 Landsdowne Street, Cambridge, MA 02139, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (FK506 BINDING PROTEIN)	A, B	107	Homo sapiens	Mutation(s): 1  Gene Names: FKBP1A, FKBP1, FKBP12 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AP1	C [auth A], D [auth B]	{3-[3-(3,4-DIMETHOXY-PHENYL)-1-(1-{1-[2-(3,4,5-TRIMETHOXY-PHENYL)-BUTYRYL]-PIPERIDIN-2YL}-VINYLOXY)-PROPYL]-PHENOXY}-ACETIC ACID C38 H47 N O11 XCCRAOPQCACRFC-OIFRRMEBSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
AP1	IC50 :  1.7999999523162842   nM  PDBBind
AP1	IC50:  1.7999999523162842   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.230 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.73	α = 62.61
b = 41.85	β = 82.75
c = 43.59	γ = 85.29

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-07-23 
• Released Date: 1998-09-02 
Deposition Author(s): Hatada, M.H., Clackson, T., Yang, W., Rozamus, L.W., Amara, J., Rollins, C.T., Stevenson, L.F., Magari, S.R., Wood, S.A., Courage, N.L., Lu, X., Cerasoli Junior, F., Gilman, M., Holt, D.

Revision History  

• Version 1.0: 1998-09-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-18
  Changes: Data collection