Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 33.61 kDa 
• Atom Count: 2,367 
• Modelled Residue Count: 273 
• Deposited Residue Count: 286 
• Unique protein chains: 1

 5EOL

Crystal structure of human Pim-1 kinase in complex with a macrocyclic quinoxaline-pyrrolodihydropiperidinone inhibitor

• PDB DOI: 10.2210/pdb5EOL/pdb

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


• Deposited: 2015-11-10 Released: 2016-05-04 
• Deposition Author(s): Mohr, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.223 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Discovery and Optimization of Macrocyclic Quinoxaline-pyrrolo-dihydropiperidinones as Potent Pim-1/2 Kinase Inhibitors.

Cee, V.J., Chavez, F., Herberich, B., Lanman, B.A., Pettus, L.H., Reed, A.B., Wu, B., Wurz, R.P., Andrews, K.L., Chen, J., Hickman, D., Laszlo, J., Lee, M.R., Guerrero, N., Mattson, B.K., Nguyen, Y., Mohr, C., Rex, K., Sastri, C.E., Wang, P., Wu, Q., Wu, T., Xu, Y., Zhou, Y., Winston, J.T., Lipford, J.R., Tasker, A.S., Wang, H.L.

(2016) ACS Med Chem Lett 7: 408-412

• PubMed: 27096050 
• DOI: 10.1021/acsmedchemlett.5b00403
• Primary Citation of Related Structures:  
  5EOL


• PubMed Abstract: 
  

The identification of Pim-1/2 kinase overexpression in B-cell malignancies suggests that Pim kinase inhibitors will have utility in the treatment of lymphoma, leukemia, and multiple myeloma. Starting from a moderately potent quinoxaline-dihydropyrrolopiperidinone lead, we recognized the potential for macrocyclization and developed a series of 13-membered macrocycles. The structure-activity relationships of the macrocyclic linker were systematically explored, leading to the identification of 9c as a potent, subnanomolar inhibitor of Pim-1 and -2. This molecule also potently inhibited Pim kinase activity in KMS-12-BM, a multiple myeloma cell line with relatively high endogenous levels of Pim-1/2, both in vitro (pBAD IC50 = 25 nM) and in vivo (pBAD EC50 = 30 nM, unbound), and a 100 mg/kg daily dose was found to completely arrest the growth of KMS-12-BM xenografts in mice.

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Organizational Affiliation: 

Amgen Inc. , One Amgen Center Drive, Thousand Oaks, California 91320-1799, United States.

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5QO	B [auth A]	macrocyclic quinoxaline-pyrrolodihydropiperidinone C21 H21 N5 O DDQXBYGNFGPJRL-CLZWFORCSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5QO	Binding MOAD:  5EOL	IC50: 0.3 (nM) from 1 assay(s)
	BindingDB:  5EOL	IC50: 0.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.223 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.856	α = 90
b = 96.856	β = 90
c = 80.452	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Mohr, C.

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release