Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 34.73 kDa 
• Atom Count: 2437 
• Residue Count: 274 
• Unique protein chains: 1

2XJ2

Protein kinase Pim-1 in complex with small molecule inhibitor

• DOI: 10.2210/pdb2XJ2/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-01 Released: 2011-02-23 
• Deposition Author(s): Schulz, M.N., Fanghanel, J., Schafer, M., Badock, V., Briem, H., Boemer, U., Nguyen, D., Husemann, M., Hillig, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.202 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

Crystallographic Fragment Screen Identifies Cinnamic Acid Derivatives as Starting Points for Potent Pim-1 Inhibitors

Schulz, M.N., Fanghanel, J., Schafer, M., Badock, V., Briem, H., Boemer, U., Nguyen, D., Husemann, M., Hillig, R.C.

(2011) Acta Crystallogr D Biol Crystallogr 67: 156

• PubMed: 21358046 
• DOI: 10.1107/S0907444910054144
• Primary Citation of Related Structures:  
  2XIX, 2XIY, 2XIZ, 2XJ0, 2XJ1, 2XJ2


• PubMed Abstract: 
  

A crystallographic fragment screen was carried out to identify starting points for the development of inhibitors of protein kinase Pim-1, a potential target for tumour therapy. All fragment hits identified via soaking in this study turned out to bind to the unusually hydrophobic pocket at the hinge region. The most potent fragments, two cinnamic acid derivatives (with a best IC(50) of 130 µM), additionally form a well defined hydrogen bond. The balance between hydrophobic and polar interactions makes these molecules good starting points for further optimization. Pim-2 inhibitors from a recently reported high-throughput screening campaign also feature a cinnamic acid moiety. Two of these Pim-2 inhibitors were synthesized, their potencies against Pim-1 were determined and their cocrystal structures were elucidated in order to determine to what degree the binding modes identified by fragment screening are conserved in optimized inhibitors. The structures show that the cinnamic acid moieties indeed adopt the same binding mode. Fragment screening thus correctly identified binding modes which are maintained when fragments are grown into larger and higher affinity inhibitors. The high-throughput screening-derived compound (E)-3-{3-[6-(4-aminocyclohexylamino)-pyrazin-2-yl]phenyl}acrylic acid (compound 1) is the most potent inhibitor of the cinnamic acid series for which the three-dimensional binding mode is known (IC(50) = 17 nM, K(d) = 28 nM). The structure reveals the molecular basis for the large gain in potency between the initial fragment hit and this optimized inhibitor.

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Organizational Affiliation: 

Bayer Schering Pharma AG, Global Drug Discovery, Berlin, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1	A	301	Homo sapiens	Mutation(s): 0  Gene Names: PIM1 EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens) Explore P11309  Go to UniProtKB:  P11309
NIH Common Fund Data Resources
PHAROS  P11309 GTEx  ENSG00000137193

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
985	A	(2E)-3-{3-[6-(4-methyl-1,4-diazepan-1-yl)pyrazin-2-yl]phenyl}prop-2-enoic acid C19 H22 N4 O2 DTBFDAJNODVUMF-VOTSOKGWSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
985	Kd:  66   nM  Binding MOAD
985	Kd :  66   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.202 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.167	α = 90
b = 96.167	β = 90
c = 80.785	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-01 
• Released Date: 2011-02-23 
Deposition Author(s): Schulz, M.N., Fanghanel, J., Schafer, M., Badock, V., Briem, H., Boemer, U., Nguyen, D., Husemann, M., Hillig, R.C.

Revision History 

• Version 1.0: 2011-02-23
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance