1YI3

Crystal Structure of Pim-1 bound to LY294002


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

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This is version 1.3 of the entry. See complete history


Literature

Pim-1 ligand-bound structures reveal the mechanism of serine/threonine kinase inhibition by LY294002.

Jacobs, M.D.Black, J.Futer, O.Swenson, L.Hare, B.Fleming, M.Saxena, K.

(2005) J Biol Chem 280: 13728-13734

  • DOI: 10.1074/jbc.M413155200
  • Primary Citation of Related Structures:  
    1YHS, 1YI3, 1YI4

  • PubMed Abstract: 
  • Pim-1 is an oncogene-encoded serine/threonine kinase primarily expressed in hematopoietic and germ cell lines. Pim-1 kinase was originally identified in Maloney murine leukemia virus-induced T-cell lymphomas and is associated with multiple cellular functions such as proliferation, survival, differentiation, apoptosis, and tumorigenesis (Wang, Z ...

    Pim-1 is an oncogene-encoded serine/threonine kinase primarily expressed in hematopoietic and germ cell lines. Pim-1 kinase was originally identified in Maloney murine leukemia virus-induced T-cell lymphomas and is associated with multiple cellular functions such as proliferation, survival, differentiation, apoptosis, and tumorigenesis (Wang, Z., Bhattacharya, N., Weaver, M., Petersen, K., Meyer, M., Gapter, L., and Magnuson, N. S. (2001) J. Vet. Sci. 2, 167-179). The crystal structures of Pim-1 complexed with staurosporine and adenosine were determined. Although a typical two-domain serine/threonine protein kinase fold is observed, the inter-domain hinge region is unusual in both sequence and conformation; a two-residue insertion causes the hinge to bulge away from the ATP-binding pocket, and a proline residue in the hinge removes a conserved main chain hydrogen bond donor. Without this hydrogen bond, van der Waals interactions with the hinge serve to position the ligand. The hinge region of Pim-1 resembles that of phosphatidylinositol 3-kinase more closely than it does other protein kinases. Although the phosphatidylinositol 3-kinase inhibitor LY294002 also inhibits Pim-1, the structure of the LY294002.Pim-1 complex reveals a new binding mode that may be general for Ser/Thr kinases.


    Organizational Affiliation

    Vertex Pharmaceuticals Incorporated, Cambridge, Massachusetts 02139, USA. marc_jacobs@vrtx.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene serine/threonine-protein kinase Pim-1A273Homo sapiensMutation(s): 2 
Gene Names: PIM1
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
PHAROS:  P11309
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LY2 (Subject of Investigation/LOI)
Query on LY2

Download Ideal Coordinates CCD File 
B [auth A]2-MORPHOLIN-4-YL-7-PHENYL-4H-CHROMEN-4-ONE
C19 H17 N O3
CZQHHVNHHHRRDU-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
AL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
LY2 BindingDB:  1YI3 IC50: min: 820, max: 4000 (nM) from 2 assay(s)
Binding MOAD:  1YI3 IC50: 4000 (nM) from 1 assay(s)
PDBBind:  1YI3 IC50: 4000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.647α = 90
b = 97.647β = 90
c = 80.725γ = 120
Software Package:
Software NamePurpose
d*TREKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description