1QVN

Structure of SP4160 Bound to IL-2 V69A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Hot-spot mimicry of a cytokine receptor by a small molecule.

Thanos, C.D.DeLano, W.L.Wells, J.A.

(2006) Proc.Natl.Acad.Sci.USA 103: 15422-15427

  • DOI: 10.1073/pnas.0607058103

  • PubMed Abstract: 
  • Protein-protein complexes remain enticing, but extremely challenging, targets for small-molecule drug discovery. In a rare example described earlier, a high-affinity small molecule, SP4206 (Kd approximately 70 nM), was found to block binding of the I ...

    Protein-protein complexes remain enticing, but extremely challenging, targets for small-molecule drug discovery. In a rare example described earlier, a high-affinity small molecule, SP4206 (Kd approximately 70 nM), was found to block binding of the IL-2alpha receptor (IL-2Ralpha) to IL-2 (Kd approximately 10 nM). Recently, the structure of the IL-2/IL-2Ralpha complex was solved [Rickert, M., Wang, X., Boulanger, M. J., Goriatcheva, N., Garcia, K. C. (2005) Science 308:1477-1480]. Using structural and functional analysis, we compare how SP4206 mimics the 83-fold larger IL-2Ralpha in binding IL-2. The binding free energy per contact atom (ligand efficiency) for SP4206 is about twice that of the receptor because of a smaller, but overlapping, contact epitope that insinuates into grooves and cavities not accessed by the receptor. Despite its independent design, the small molecule has a similar, but more localized, charge distribution compared with IL-2Ralpha. Mutational studies show that SP4206 targets virtually the same critical "hot-spot" residues on IL-2 that drive binding of IL-2Ralpha. Moreover, a mutation that enhances binding to the IL-2Ralpha near these hot spots also enhances binding to SP4206. Although the protein and small molecule do bind the same hot spot, they trap very different conformations of IL-2 because of its flexible nature. Our studies suggest that precise structural mimics of receptors are not required for high-affinity binding of small molecules, and they show that there are multiple solutions to tight binding at shared and adaptive hot spots.


    Organizational Affiliation

    Sunesis Pharmaceuticals, 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-2
A, B, C, D
132Homo sapiensMutation(s): 1 
Gene Names: IL2
Find proteins for P60568 (Homo sapiens)
Go to Gene View: IL2
Go to UniProtKB:  P60568
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FRI
Query on FRI

Download SDF File 
Download CCD File 
A, B, C, D
2-GUANIDINO-4-METHYL-PENTANOIC ACID [2-(4-{5-[4-(4-ACETYLAMINO-BENZYLOXY)-2,3-DICHLORO-PHENYL]-2-METHYL-2H-PYRAZOL-3-YL}-PIPERIDIN-1-YL)-2-OXO-ETHYL]-AMIDE
SP4160
C33 H42 Cl2 N8 O4
VCXMTWSYQSVWRK-AREMUKBSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.258 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.514α = 90.00
b = 85.134β = 90.00
c = 122.141γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-05
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-01-09
    Type: Database references