Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.94 kDa 
• Atom Count: 2426 
• Modelled Residue Count: 274 
• Deposited Residue Count: 321 
• Unique protein chains: 2

2C3I

CRYSTAL STRUCTURE OF HUMAN PIM1 IN COMPLEX WITH IMIDAZOPYRIDAZIN I

• PDB DOI: 10.2210/pdb2C3I/pdb

• Classification: TRANSFERASE/PEPTIDE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2005-10-07 Released: 2005-11-01 
• Deposition Author(s): Philippakopoulos, P., Knapp, S., Debreczeni, J., Bullock, A., von Delft, F., Sundstrom, M., Arrowsmith, C., Edwards, A., Guo, K., Weigelt, J.

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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 

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

• PubMed: 17638903 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PIMTIDE	A	8	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE SERINE THREONINE PROTEIN KINASE PIM1	B	313	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IYZ	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
ID	Source	Binding Affinity
IYZ	Binding MOAD:  2C3I	Kd: 25 (nM) from 1 assay(s)
	BindingDB:  2C3I	Kd: 25 (nM) from 1 assay(s)
		IC50: min: 61, max: 120 (nM) from 2 assay(s)
		-TΔS: -1.95e+1 (kJ/mol) from 1 assay(s)
		ΔG: -4.10e+1 (kJ/mol) from 1 assay(s)
	PDBBind:  2C3I	Kd: 25 (nM) 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 = 98.439	α = 90
b = 98.439	β = 90
c = 80.843	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-07 
• Released Date: 2005-11-01 
Deposition Author(s): Philippakopoulos, P., Knapp, S., Debreczeni, J., Bullock, A., von Delft, F., Sundstrom, M., Arrowsmith, C., Edwards, A., Guo, K., Weigelt, J.

Revision History  

• 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