Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 36.07 kDa 
• Atom Count: 2445 
• Modelled Residue Count: 273 
• Deposited Residue Count: 312 
• Unique protein chains: 1

2J2I

Crystal Structure of the humab PIM1 in complex with LY333531

• DOI: 10.2210/pdb2J2I/pdb

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


• Deposited: 2006-08-16 Released: 2007-02-13 
• Deposition Author(s): Debreczeni, J.E., Bullock, A.N., von Delft, F., Sundstrom, M., Arrowsmith, C., Edwards, A., Weigelt, J., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.200 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Literature

A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases.

Fedorov, O., Marsden, B., Pogacic, V., Rellos, P., Muller, S., Bullock, A.N., Schwaller, J., Sundstrom, M., Knapp, S.

(2007) Proc Natl Acad Sci U S A 104: 20523-20528

• PubMed: 18077363 
• DOI: 10.1073/pnas.0708800104
• Primary Citation of Related Structures:  
  2J2I


• PubMed Abstract: 
  

Protein kinases play a pivotal role in cell signaling, and dysregulation of many kinases has been linked to disease development. A large number of kinase inhibitors are therefore currently under investigation in clinical trials, and so far seven inhibitors have been approved as anti-cancer drugs. In addition, kinase inhibitors are widely used as specific probes to study cell signaling, but systematic studies describing selectivity of these reagents across a panel of diverse kinases are largely lacking. Here we evaluated the specificity of 156 validated kinase inhibitors, including inhibitors used in clinical trials, against 60 human Ser/Thr kinases using a thermal stability shift assay. Our analysis revealed many unexpected cross-reactivities for inhibitors thought to be specific for certain targets. We also found that certain combinations of active-site residues in the ATP-binding site correlated with the detected ligand promiscuity and that some kinases are highly sensitive to inhibition using diverse chemotypes, suggesting them as preferred intervention points. Our results uncovered also inhibitor cross-reactivities that may lead to alternate clinical applications. For example, LY333'531, a PKCbeta inhibitor currently in phase III clinical trials, efficiently inhibited PIM1 kinase in our screen, a suggested target for treatment of leukemia. We determined the binding mode of this inhibitor by x-ray crystallography and in addition showed that LY333'531 induced cell death and significantly suppressed growth of leukemic cells from acute myeloid leukemia patients.

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Organizational Affiliation: 

Structural Genomics Consortium, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1	A [auth B]	312	Homo sapiens	Mutation(s): 1  Gene Names: PIM1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens) Explore P11309  Go to UniProtKB:  P11309
PHAROS:  P11309 GTEx:  ENSG00000137193

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LY4 (Subject of Investigation/LOI)	C [auth B]	(9R)-9-[(DIMETHYLAMINO)METHYL]-6,7,10,11-TETRAHYDRO-9H,18H-5,21:12,17-DIMETHENODIBENZO[E,K]PYRROLO[3,4-H][1,4,13]OXADIA ZACYCLOHEXADECINE-18,20-DIONE C28 H28 N4 O3 ZCBUQCWBWNUWSU-SFHVURJKSA-N
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
LY4	BindingDB:  2J2I	Kd: min: 50, max: 270 (nM) from 3 assay(s)
		IC50: 200 (nM) from 1 assay(s)
	Binding MOAD:  2J2I	IC50: 200 (nM) from 1 assay(s)
	PDBBind:  2J2I	IC50: 200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.200 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.157	α = 90
b = 98.157	β = 90
c = 80.366	γ = 120

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2006-08-16 
• Released Date: 2007-02-13 
Deposition Author(s): Debreczeni, J.E., Bullock, A.N., von Delft, F., Sundstrom, M., Arrowsmith, C., Edwards, A., Weigelt, J., Knapp, S.

Revision History  

• Version 1.0: 2007-02-13
  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: 2018-02-28
  Changes: Database references, Source and taxonomy
• Version 1.4: 2018-04-04
  Changes: Data collection
• Version 1.5: 2019-03-06
  Changes: Data collection, Experimental preparation
• Version 1.6: 2019-05-08
  Changes: Data collection, Experimental preparation