1PW6

Low Micromolar Small Molecule Inhibitor of IL-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Potent small-molecule binding to a dynamic hot spot on IL-2.

Thanos, C.D.Randal, M.Wells, J.A.

(2003) J.Am.Chem.Soc. 125: 15280-15281

  • DOI: 10.1021/ja0382617
  • Primary Citation of Related Structures:  1PY2

  • PubMed Abstract: 
  • The complexes between IL-2 and two similar small molecules, one a lead compound and the other a potent, affinity-optimized compound, were determined by X-ray crystallography. The lead compound (IC50 = 6 muM) bound to a hot spot on IL-2 in a groove th ...

    The complexes between IL-2 and two similar small molecules, one a lead compound and the other a potent, affinity-optimized compound, were determined by X-ray crystallography. The lead compound (IC50 = 6 muM) bound to a hot spot on IL-2 in a groove that is not apparent in either the unliganded protein or a complex between IL-2 and a weakly bound drug fragment. The affinity-optimized compound (IC50 = 0.06 muM), which has an added aromatic acid fragment, bound in the same groove as the lead compound. In addition, a novel binding site was formed for the aromatic acid which is unseen in the complex with the lead compound. Thus, the hot spot on IL-2 is highly dynamic, with the protein changing form at multiple sites to maximize packing for each compound. Binding-site rigidity is often thought to play a role in high-affinity interactions. However, in this case, specific contacts between the small molecule and the protein are made despite the adaptivity of the hot spot. Given the change in morphology that was observed in IL-2, it is unlikely that a potent inhibitor could have been found by rational design. Therefore, fragment assembly methods offer the stochastic advantage of finding fragments in flexible protein regions where structural changes are unpredictable.


    Organizational Affiliation

    Sunesis Pharmaceuticals, Inc., 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
133Homo sapiensGene 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FRB
Query on FRB

Download SDF File 
Download CCD File 
A, B
2-CYCLOHEXYL-N-(2-{4-[5-(2,3-DICHLORO-PHENYL)-2H-PYRAZOL-3-YL]-PIPERIDIN-1-YL}-2-OXO-ETHYL)-2-GUANIDINO-ACETAMIDE
SP2456
C25 H33 Cl2 N7 O2
SSSXBBASYYVGCI-HSZRJFAPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FRBIC50: 6000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.258 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.889α = 90.00
b = 79.889β = 90.00
c = 171.891γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-13
    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: 2017-10-11
    Type: Refinement description