Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.18 kDa 
• Atom Count: 2422 
• Modelled Residue Count: 273 
• Deposited Residue Count: 314 
• Unique protein chains: 1

4BZN

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

• DOI: 10.2210/pdb4BZN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-29 Released: 2013-10-30 
• Deposition Author(s): Casale, E., Casuscelli, F., Ardini, E., Avanzi, N., 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.

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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 

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

• PubMed: 24139169 
• 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. 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.

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Organizational Affiliation: 

Oncology, Nerviano Medical Sciences, viale Pasteur 10, 20014 Nerviano (MI), Italy. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE PIM-1	A	314	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UGX (Subject of Investigation/LOI)	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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Binding Affinity Annotations
ID	Source	Binding 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 = 96.802	α = 90
b = 96.802	β = 90
c = 79.995	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2013-07-29 
• Released Date: 2013-10-30 
Deposition Author(s): Casale, E., Casuscelli, F., Ardini, E., Avanzi, N., 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.

Revision History  

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