2C3I

CRYSTAL STRUCTURE OF HUMAN PIM1 IN COMPLEX WITH IMIDAZOPYRIDAZIN I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural Analysis Identifies Imidazo[1,2- B]Pyridazines as Pim Kinase Inhibitors with in Vitro Antileukemic Activity.

Pogacic, V.Bullock, A.N.Fedorov, O.Filippakopoulos, P.Gasser, C.Biondi, A.Meyer-Monard, S.Knapp, S.Schwaller, J.

(2007) Cancer Res 67: 6916

  • DOI: https://doi.org/10.1158/0008-5472.CAN-07-0320
  • Primary Citation of Related Structures:  
    2C3I

  • PubMed Abstract: 

    Much attention has recently been focused on PIM kinases as potential targets for the treatment of hematopoietic malignancies and some solid cancers. Using protein stability shift assays, we identified a family of imidazo[1,2-b]pyridazines to specifically interact with and inhibit PIM kinases with low nanomolar potency. The high-resolution crystal structure of a PIM1 inhibitor complex revealed that imidazo[1,2-b]pyridazines surprisingly interact with the NH(2)-terminal lobe helix alphaC rather than with the kinase hinge region. Thus, the identified inhibitors are ATP competitive but not ATP mimetic compounds, explaining their enhanced selectivity with respect to conventional type I kinase inhibitors. One of the identified imidazo[1,2-b]pyridazines (K00135) was further tested in several hematopoietic cellular systems. First, K00135 dose-dependently impaired survival of murine Ba/F3 cells that have been rendered cytokine independent by overexpression of human PIMs. Second, K00135 impaired survival and clonogenic growth of a panel of human acute leukemia cells. Third, exposure of K00135 significantly suppressed in vitro growth of leukemic blasts from five acute myelogenous leukemia patients but not of normal umbilical cord blood mononuclear cells. In vitro kinase assays and immunoblotting using lysates from human MV4;11 leukemic cells showed inhibition of phosphorylation of known PIM downstream targets, such as BAD and eukaryotic translation initiation factor 4E-binding protein 1, by K00135. Taken together, we report a family of small molecules that selectively interact and block PIM kinases and could serve as a lead to develop new targeted antileukemic therapeutics.


  • Organizational Affiliation

    Department of Research and the Hematology Clinic, University Hospital Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PIMTIDE8Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTO-ONCOGENE SERINE THREONINE PROTEIN KINASE PIM1313Homo sapiensMutation(s): 1 
EC: 2.7.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
PHAROS:  P11309
GTEx:  ENSG00000137193 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11309
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IYZ
Query on IYZ

Download Ideal Coordinates CCD File 
C [auth B]1-(3-{6-[(CYCLOPROPYLMETHYL)AMINO]IMIDAZO[1,2-B]PYRIDAZIN-3-YL}PHENYL)ETHANONE
C18 H18 N4 O
IVUBNTNWKIPCPS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
IYZ PDBBind:  2C3I Kd: 25 (nM) from 1 assay(s)
BindingDB:  2C3I Kd: 25 (nM) from 1 assay(s)
IC50: min: 12, max: 120 (nM) from 3 assay(s)
-TΔS: -1.95e+1 (kJ/mol) from 1 assay(s)
ΔG: -4.10e+1 (kJ/mol) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.439α = 90
b = 98.439β = 90
c = 80.843γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description