5IPJ

Crystal structure of human Pim-1 kinase in complex with a quinazolinone-pyrrolopyrrolone inhibitor.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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Literature

Discovery and Optimization of Quinazolinone-pyrrolopyrrolones as Potent and Orally Bioavailable Pan-Pim Kinase Inhibitors.

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

(2016) J Med Chem 59: 6407-6430

  • DOI: 10.1021/acs.jmedchem.6b00610
  • Primary Citation of Related Structures:  
    5IPJ

  • PubMed Abstract: 

    • The high expression of proviral insertion site of Moloney murine leukemia virus kinases (Pim-1, -2, and -3) in cancers, particularly the hematopoietic malignancies, is believed to play a role in promoting cell survival and proliferation while suppressing apoptosis ...

    The high expression of proviral insertion site of Moloney murine leukemia virus kinases (Pim-1, -2, and -3) in cancers, particularly the hematopoietic malignancies, is believed to play a role in promoting cell survival and proliferation while suppressing apoptosis. The three isoforms of Pim protein appear largely redundant in their oncogenic functions. Thus, a pan-Pim kinase inhibitor is highly desirable. However, cell active pan-Pim inhibitors have proven difficult to develop because Pim-2 has a low Km for ATP and therefore requires a very potent inhibitor to effectively block the kinase activity at cellular ATP concentrations. Herein, we report a series of quinazolinone-pyrrolopyrrolones as potent and selective pan-Pim inhibitors. In particular, compound 17 is orally efficacious in a mouse xenograft model (KMS-12 BM) of multiple myeloma, with 93% tumor growth inhibition at 50 mg/kg QD upon oral dosing.

    Organizational Affiliation: 

    Department of Therapeutic Discovery-Medicinal Chemistry, ‡Molecular Structure, §Pharmacokinetics and Drug Metabolism, ∥Oncology Research, ⊥Pharmaceutics, #Discovery Technologies, Amgen Inc. , One Amgen Center Drive, Thousand Oaks, California 91320, United States.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1A286Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11309
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6CD
Query on 6CD
Download Ideal Coordinates CCD File 
B [auth A]2-(tert-butylamino)-3-methyl-8-[(6R)-6-methyl-4-oxo-1,4,5,6-tetrahydropyrrolo[3,4-b]pyrrol-2-yl]quinazolin-4(3H)-one
C20 H23 N5 O2
HLPARXMUJBJYFM-SNVBAGLBSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
6CD Binding MOAD:  5IPJ Kd: 1.3 (nM) from 1 assay(s)
BindingDB:  5IPJ Kd: 1.3 (nM) from 1 assay(s)
IC50: min: 0.3, max: 0.78 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.408α = 90
b = 97.408β = 90
c = 80.663γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2016-06-22 
    • Deposition Author(s): Mohr, C.

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-07-27
    Changes: Database references