1M4B

Crystal Structure of Human Interleukin-2 K43C Covalently Modified at C43 with 2-[2-(2-Cyclohexyl-2-guanidino-acetylamino)-acetylamino]-N-(3-mercapto-propyl)-propionamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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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 U S A 100: 1603-1608

  • DOI: https://doi.org/10.1073/pnas.252756299
  • Primary Citation of Related Structures:  
    1M47, 1M48, 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
interleukin-2133Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P60568 (Homo sapiens)
Explore P60568 
Go to UniProtKB:  P60568
PHAROS:  P60568
GTEx:  ENSG00000109471 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60568
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NMP
Query on NMP

Download Ideal Coordinates CCD File 
B [auth A]2-[2-(2-CYCLOHEXYL-2-GUANIDINO-ACETYLAMINO)-ACETYLAMINO]-N-(3-MERCAPTO-PROPYL)-PROPIONAMIDE
C17 H32 N6 O3 S
YLLNYDDZOMCFDE-SMDDNHRTSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.247 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.488α = 90
b = 35.102β = 97.52
c = 36.642γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
AMoREphasing
REFMACrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NMPClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-31
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations