4WRS | pdb_00004wrs

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

• PDB DOI: https://doi.org/10.2210/pdb4WRS/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 2.20 Å
• R-Value Free: 
  0.208 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

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: https://doi.org/10.1016/j.bmcl.2014.12.068
• Primary Citation Related Structures: 
  4RPV, 4WRS


• 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].
Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA. Electronic address: [e-mail].
Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA.
Department of Oncology, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA.
Department of Molecular Structure and Characterization, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA.
Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 33.68 kDa 
• Atom Count: 2,411 
• Modeled Residue Count: 273 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	286	Homo sapiens	Mutation(s): 0  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
3U1	D [auth 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	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3U1	BindingDB:  4WRS	IC50: min: 0.4, max: 1 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.208 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.815	α = 90
b = 97.815	β = 90
c = 80.585	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary