Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.94 kDa 
• Atom Count: 2,459 
• Modelled Residue Count: 274 
• Deposited Residue Count: 328 
• Unique protein chains: 1

 4N6Y

Pim1 Complexed with a phenylcarboxamide

• PDB DOI: 10.2210/pdb4N6Y/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-10-14 Released: 2013-11-06 
• Deposition Author(s): Bellamacina, C.R., Le, V., Shu, W., Burger, M.T., Bussiere, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.212 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 

Literature

Structure Guided Optimization, in Vitro Activity, and in Vivo Activity of Pan-PIM Kinase Inhibitors.

Burger, M.T., Han, W., Lan, J., Nishiguchi, G., Bellamacina, C., Lindval, M., Atallah, G., Ding, Y., Mathur, M., McBride, C., Beans, E.L., Muller, K., Tamez, V., Zhang, Y., Huh, K., Feucht, P., Zavorotinskaya, T., Dai, Y., Holash, J., Castillo, J., Langowski, J., Wang, Y., Chen, M.Y., Garcia, P.D.

(2013) ACS Med Chem Lett 4: 1193-1197

• PubMed: 24900629 
• DOI: 10.1021/ml400307j
• Primary Citation of Related Structures:  
  4N6Y, 4N6Z, 4N70


• PubMed Abstract: 
  

Proviral insertion of Moloney virus (PIM) 1, 2, and 3 kinases are serine/threonine kinases that normally function in survival and proliferation of hematopoietic cells. As high expression of PIM1, 2, and 3 is frequently observed in many human malignancies, including multiple myeloma, non-Hodgkins lymphoma, and myeloid leukemias, there is interest in determining whether selective PIM inhibition can improve outcomes of these human cancers. Herein, we describe our efforts toward this goal. The structure guided optimization of a singleton high throughput screening hit in which the potency against all three PIM isoforms was increased >10,000-fold to yield compounds with pan PIM K is < 10 pM, nanomolar cellular potency, and in vivo activity in an acute myeloid leukemia Pim-dependent tumor model is described.

---

Organizational Affiliation: 

Oncology Research, Novartis Institutes for Biomedical Research , 4560 Horton Street, Emeryville, California 94608, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	328	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2HV	B [auth A]	2-(acetylamino)-N-[2-(piperidin-1-yl)phenyl]-1,3-thiazole-4-carboxamide C17 H20 N4 O2 S XPDNPGNUQDMFOW-UHFFFAOYSA-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
2HV	BindingDB:  4N6Y	Ki: min: 90, max: 92 (nM) from 2 assay(s)
	PDBBind:  4N6Y	Ki: 92 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.212 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.875	α = 90
b = 97.875	β = 90
c = 80.454	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-06 
Deposition Author(s): Bellamacina, C.R., Le, V., Shu, W., Burger, M.T., Bussiere, D.

Revision History  

• Version 1.0: 2013-11-06
  Type: Initial release
  
• Version 1.1: 2014-07-02
  Changes: Database references