4BZN

Crystal structure of PIM1 in complex with a Pyrrolo(1,2-a)Pyrazinone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


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:  
    4BZN, 4BZO

  • 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 range ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE PIM-1A314Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UGX (Subject of Investigation/LOI)
Query on UGX

Download Ideal Coordinates CCD File 
B [auth A]N-(2,2-dimethylpropyl)-2-[1-oxo-7-(thiophen-3-yl)-1,2,3,4-tetrahydropyrrolo[1,2-a]pyrazin-4-yl]acetamide
C18 H23 N3 O2 S
PNMQDIXULZYDDT-AWEZNQCLSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
UGX BindingDB:  4BZN IC50: 1441 (nM) from 1 assay(s)
Binding MOAD:  4BZN IC50: 1441 (nM) from 1 assay(s)
PDBBind:  4BZN IC50: 1441 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.802α = 90
b = 96.802β = 90
c = 79.995γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

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