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 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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: https://doi.org/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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1286Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11309
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding 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 = 96.856α = 90
b = 96.856β = 90
c = 80.452γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Derived calculations