4BZO

Crystal structure of PIM1 in complex with a Pyrrolo-Pyrazinone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery and Optimization of Pyrrolo[1,2-A]Pyrazinones Leads to Novel and Selective Inhibitors of Pim Kinases.

Casuscelli, F.Ardini, E.Avanzi, N.Casale, E.Cervi, G.D'Anello, M.Donati, D.Faiardi, D.Ferguson, R.D.Fogliatto, G.Galvani, A.Marsiglio, A.Mirizzi, D.G.Montemartini, M.Orrenius, C.Papeo, G.Piutti, C.Salom, B.Felder, E.R.

(2013) Bioorg.Med.Chem. 21: 7364

  • DOI: 10.1016/j.bmc.2013.09.054
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A novel series of PIM inhibitors was derived from a combined effort in natural product-inspired library generation and screening. The novel pyrrolo[1,2-a]pyrazinones initial hits are inhibitors of PIM isoforms with IC50 values in the low micromolar r ...

    A novel series of PIM inhibitors was derived from a combined effort in natural product-inspired library generation and screening. The novel pyrrolo[1,2-a]pyrazinones initial hits are inhibitors of PIM isoforms with IC50 values in the low micromolar range. The application of a rational optimization strategy, guided by the determination of the crystal structure of the complex in the kinase domain of PIM1 with compound 1, led to the discovery of compound 15a, which is a potent PIM kinases inhibitor exhibiting excellent selectivity against a large panel of kinases, representative of each family. The synthesis, structure-activity relationship studies, and pharmacokinetic data of compounds from this inhibitor class are presented herein. Furthermore, the cellular activities including inhibition of cell growth and modulation of downstream targets are also described.


    Organizational Affiliation

    Oncology, Nerviano Medical Sciences, viale Pasteur 10, 20014 Nerviano (MI), Italy. Electronic address: francesco.casuscelli@nervianoms.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE/THREONINE-PROTEIN KINASE PIM-1
A
314Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
676
Query on 676

Download SDF File 
Download CCD File 
A
N-[(1S)-2-AMINO-1-PHENYLETHYL]-2-[(4S)-7-(2-FLUORO-4-PYRIDINYL)-1-OXO-1,2,3,4-TETRAHYDROPYRROLO[1,2-A]PYRAZIN-4-YL]ACETAMIDE
C22 H22 F N5 O2
MCZCAWWHZGEUFE-ZWKOTPCHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
676IC50: 13 nM (99) BINDINGDB
676IC50: 13 nM BINDINGMOAD
676IC50: 13 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.181 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 97.932α = 90.00
b = 97.932β = 90.00
c = 81.431γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2013-11-13
    Type: Database references