Biological Assembly 1  

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

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

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

Macromolecule Content

• Total Structure Weight: 34.83 kDa 
• Atom Count: 2460 
• Modelled Residue Count: 273 
• Deposited Residue Count: 299 
• Unique protein chains: 1

5DIA

PIM1 in complex with Cpd36 ((1S,3S)-N1-(6-(5-(pyridin-3-yl)-1H-pyrazolo[3,4-c]pyridin-3-yl)pyridin-2-yl)cyclohexane-1,3-diamine)

• DOI: 10.2210/pdb5DIA/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-08-31 Released: 2015-10-28 
• Deposition Author(s): Murray, J.M., Wallweber, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.229 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Literature

Discovery of 3,5-substituted 6-azaindazoles as potent pan-Pim inhibitors.

Hu, H., Wang, X., Chan, G.K., Chang, J.H., Do, S., Drummond, J., Ebens, A., Lee, W., Ly, J., Lyssikatos, J.P., Murray, J., Moffat, J.G., Chao, Q., Tsui, V., Wallweber, H., Kolesnikov, A.

(2015) Bioorg Med Chem Lett 25: 5258-5264

• PubMed: 26459208 
• DOI: 10.1016/j.bmcl.2015.09.052
• Primary Citation of Related Structures:  
  5DGZ, 5DHJ, 5DIA


• PubMed Abstract: 
  

Pim kinase inhibitors are promising cancer therapeutics. Pim-2, among the three Pim isoforms, plays a critical role in multiple myeloma yet inhibition of Pim-2 is challenging due to its high affinity for ATP. A co-crystal structure of a screening hit 1 bound to Pim-1 kinase revealed the key binding interactions of its indazole core within the ATP binding site. Screening of analogous core fragments afforded 1H-pyrazolo[3,4-c]pyridine (6-azaindazole) as a core for the development of pan-Pim inhibitors. Fragment and structure based drug design led to identification of the series with picomolar biochemical potency against all three Pim isoforms. Desirable cellular potency was also achieved.

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Organizational Affiliation: 

Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	299	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
5E6 (Subject of Investigation/LOI)	B [auth A]	(1S,3S)-N-{6-[5-(pyridin-3-yl)-1H-pyrazolo[3,4-c]pyridin-3-yl]pyridin-2-yl}cyclohexane-1,3-diamine C22 H23 N7 FWMVELRLCYRLLJ-HOTGVXAUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5E6	BindingDB:  5DIA	Ki: 0.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.229 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.079	α = 90
b = 97.079	β = 90
c = 80.687	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2015-08-31 
• Released Date: 2015-10-28 
Deposition Author(s): Murray, J.M., Wallweber, H.

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2015-11-11
  Changes: Database references