Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.88 kDa 
• Atom Count: 998 
• Residue Count: 110 
• Unique protein chains: 2

1BHF

P56LCK SH2 DOMAIN INHIBITOR COMPLEX

• DOI: 10.2210/pdb1BHF/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-06-08 Released: 1998-10-21 
• Deposition Author(s): Tong, L., Warren, T.C., Lukas, S., Schembri-King, J., Betageri, R., Proudfoot, J.R., Jakes, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

Carboxymethyl-phenylalanine as a replacement for phosphotyrosine in SH2 domain binding.

Tong, L., Warren, T.C., Lukas, S., Schembri-King, J., Betageri, R., Proudfoot, J.R., Jakes, S.

(1998) J Biol Chem 273: 20238-20242

• PubMed: 9685372 
• DOI: 10.1074/jbc.273.32.20238
• Primary Citation of Related Structures:  
  1BHH, 1BHF


• PubMed Abstract: 
  

The crystal structure of human p56(lck) SH2 domain in complex with an inhibitor containing the singly charged p-(carboxymethyl)phenylalanine residue (cmF) as a phosphotyrosine (Tyr(P) or pY) replacement has been determined at 1.8 A resolution. The binding mode of the acetyl-cmF-Glu-Glu-Ile (cmFEEI) inhibitor is very similar to that of the pYEEI inhibitor, confirming that the cmFEEI inhibitor has a similar mechanism of SH2 domain inhibition despite its significantly reduced potency. Observed conformational differences in the side chain of the cmF residue can be interpreted in terms of maintaining similar interactions with the SH2 domain as the Tyr(P) residue. The crystal structure of the free p56(lck) SH2 domain has been determined at 1.9 A resolution and shows an open conformation for the BC loop and an open phosphotyrosine binding pocket, in contrast to earlier studies on the src SH2 domain that showed mostly closed conformation. The structural information presented here suggests that the carboxymethyl-phenylalanine residue may be a viable Tyr(P) replacement and represents an attractive starting point for the design and development of SH2 domain inhibitors with better pharmaceutical profiles.

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Organizational Affiliation: 

Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut 06877, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-LYMPHOCYTE-SPECIFIC PROTEIN TYROSINE KINASE P56LCK	A	108	Homo sapiens	Mutation(s): 0  Gene Names: LCK EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
Find proteins for P06239 (Homo sapiens) Explore P06239  Go to UniProtKB:  P06239
NIH Common Fund Data Resources
PHAROS:  P06239 GTEx:  ENSG00000182866

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
INHIBITOR ACE-IPA-GLU-GLU-ILE	I	5	N/A	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
1PA	I	L-PEPTIDE LINKING	C11 H13 N O4		PHE

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000406	I	ACE-IPA-GLU-GLU-ILE	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.7	α = 90
b = 45.2	β = 90
c = 26.1	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
RIGAKU	data reduction
RIGAKU	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-06-08 
• Released Date: 1998-10-21 
Deposition Author(s): Tong, L., Warren, T.C., Lukas, S., Schembri-King, J., Betageri, R., Proudfoot, J.R., Jakes, S.

Revision History 

• Version 1.0: 1998-10-21
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other