1M48

Crystal Structure of Human IL-2 Complexed with (R)-N-[2-[1-(Aminoiminomethyl)-3-piperidinyl]-1-oxoethyl]-4-(phenylethynyl)-L-phenylalanine methyl ester


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Binding of small molecules to an adaptive protein-protein interface

Arkin, M.A.Randal, M.DeLano, W.L.Hyde, J.Luong, T.N.Oslob, J.D.Raphael, D.R.Taylor, L.Wang, J.McDowell, R.S.Wells, J.A.Braisted, A.C.

(2003) Proc.Natl.Acad.Sci.USA 100: 1603-1608

  • DOI: 10.1073/pnas.252756299
  • Primary Citation of Related Structures:  1M47, 1M49, 1M4A, 1M4B, 1M4C

  • PubMed Abstract: 
  • Understanding binding properties at protein-protein interfaces has been limited to structural and mutational analyses of natural binding partners or small peptides identified by phage display. Here, we present a high-resolution analysis of a nonpepti ...

    Understanding binding properties at protein-protein interfaces has been limited to structural and mutational analyses of natural binding partners or small peptides identified by phage display. Here, we present a high-resolution analysis of a nonpeptidyl small molecule, previously discovered by medicinal chemistry [Tilley, J. W., et al. (1997) J. Am. Chem. Soc. 119, 7589-7590], which binds to the cytokine IL-2. The small molecule binds to the same site that binds the IL-2 alpha receptor and buries into a groove not seen in the free structure of IL-2. Comparison of the bound and several free structures shows this site to be composed of two subsites: one is rigid, and the other is highly adaptive. Thermodynamic data suggest the energy barriers between these conformations are low. The subsites were dissected by using a site-directed screening method called tethering, in which small fragments were captured by disulfide interchange with cysteines introduced into IL-2 around these subsites. X-ray structures with the tethered fragments show that the subsite-binding interactions are similar to those observed with the original small molecule. Moreover, the adaptive subsite tethered many more compounds than did the rigid one. Thus, the adaptive nature of a protein-protein interface provides sites for small molecules to bind and underscores the challenge of applying structure-based design strategies that cannot accurately predict a dynamic protein surface.


    Organizational Affiliation

    Department of Biology, Sunesis Pharmaceuticals, South San Francisco, CA 94080-1913, USA. mra@sunesis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
interleukin-2
A, B
133Homo sapiensGene Names: IL2
Find proteins for P60568 (Homo sapiens)
Go to Gene View: IL2
Go to UniProtKB:  P60568
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FRG
Query on FRG

Download SDF File 
Download CCD File 
A, B
2-[3-METHYL-4-(N-METHYL-GUANIDINO)-BUTYRYLAMINO]-3-(4-PHENYLETHYNYL-PHENYL)-PROPIONIC ACID METHYL ESTER
(R)-N-[2-[1-(AMINOIMINOMETHYL)-3-PIPERIDINYL]-1-OXOETHYL]-4-(PHENYLETHYNYL)-L-PHENYLALANINE METHYL ESTER
C26 H30 N4 O3
MRNGXYMKYHNMLV-PKTZIBPZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FRGKd: 8200 nM BINDINGMOAD
FRGKd: 8200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.470α = 90.00
b = 58.020β = 90.00
c = 93.080γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
d*TREKdata reduction
d*TREKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-07-31
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description