1BHF

P56LCK SH2 DOMAIN INHIBITOR COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • Primary Citation of Related Structures:  1BHH

  • 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 bi ...

    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.


    Organizational Affiliation

    Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut 06877, USA. tong@como.bio.columbia.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-LYMPHOCYTE-SPECIFIC PROTEIN TYROSINE KINASE P56LCK
A
108Homo sapiensGene Names: LCK
EC: 2.7.10.2
Find proteins for P06239 (Homo sapiens)
Go to Gene View: LCK
Go to UniProtKB:  P06239
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INHIBITOR ACE-IPA-GLU-GLU-ILE
I
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000406
Query on PRD_000406
IACE-IPA-GLU-GLU-ILEPeptide-like / Inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 80.700α = 90.00
b = 45.200β = 90.00
c = 26.100γ = 90.00
Software Package:
Software NamePurpose
RIGAKUdata reduction
RIGAKUdata scaling
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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