Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 33682.06 
• Atom Count: 2269 
• Residue Count: 286 
• Unique protein chains: 1

4WRS

Crystal structure of human Pim-1 kinase in complex with an azaspiro pyrazinyl-indazole inhibitor.

• DOI: 10.2210/pdb4WRS/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2014-10-25 Released: 2015-02-04 
• Deposition Author(s): Mohr, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.208 
• R-Value Work: 0.179 

Literature

The discovery of novel 3-(pyrazin-2-yl)-1H-indazoles as potent pan-Pim kinase inhibitors.

Wang, H.L., Cee, V.J., Chavez, F., Lanman, B.A., Reed, A.B., Wu, B., Guerrero, N., Lipford, J.R., Sastri, C., Winston, J., Andrews, K.L., Huang, X., Lee, M.R., Mohr, C., Xu, Y., Zhou, Y., Tasker, A.S.

(2015) Bioorg.Med.Chem.Lett. 25: 834-840

• PubMed: 25597005 
• DOI: 10.1016/j.bmcl.2014.12.068
• Primary Citation of Related Structures:  
  4RPV


• PubMed Abstract: 
  

The three Pim kinases are a small family of serine/threonine kinases regulating several signaling pathways that are fundamental to tumorigenesis. As such, the Pim kinases are a very attractive target for pharmacological inhibition in cancer therapy. Herein, we describe our efforts toward the development of a potent, pan-Pim inhibitor. The synthesis and hit-to-lead SAR development from a 3-(pyrazin-2-yl)-1H-indazole derived hit 2 to the identification of a series of potent, pan-Pim inhibitors such as 13o are described.

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Organizational Affiliation: 

Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA. Electronic address: [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Serine/threonine-protein kinase pim-1	A	286	Homo sapiens	Mutation(s): 0  Gene Names: PIM1 EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens) Go to Gene View: PIM1 Go to UniProtKB:  P11309

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
3U1	A	3-{6-[(4R)-6-azaspiro[2.5]oct-4-yloxy]pyrazin-2-yl}-5-(2,6-difluorophenyl)-1H-indazole C24 H21 F2 N5 O FCGLYPSBPNFQRF-FQEVSTJZSA-N
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
3U1	IC50: 0.4 - 1 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.208 
• R-Value Work: 0.179 
• Space Group: P 6₅

Unit Cell:

Length (Å)	Angle (°)
a = 97.815	α = 90.00
b = 97.815	β = 90.00
c = 80.585	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-10-25 
• Released Date: 2015-02-04 
• Deposition Author(s): Mohr, C.

Revision History 

• Version 1.0: 2015-02-04
  Type: Initial release
• Version 1.1: 2015-02-11
  Type: Database references