5EOL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1021/acsmedchemlett.5b00403

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase pim-1
A
286Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
5QO
Query on 5QO

Download SDF File 
Download CCD File 
A
macrocyclic quinoxaline-pyrrolodihydropiperidinone
C21 H21 N5 O
DDQXBYGNFGPJRL-CLZWFORCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 96.856α = 90.00
b = 96.856β = 90.00
c = 80.452γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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