5EOL

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


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 

wwPDB Validation 3D Report Full Report



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

  • 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-dihydropyrrol ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1A286Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5QO
Query on 5QO

Download CCD File 
A
macrocyclic quinoxaline-pyrrolodihydropiperidinone
C21 H21 N5 O
DDQXBYGNFGPJRL-CLZWFORCSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5QOIC50:  0.30000001192092896   nM  Binding MOAD
5QOIC50:  0.30000001192092896   nM  BindingDB
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 = 96.856α = 90
b = 96.856β = 90
c = 80.452γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History 

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