Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 34832.61 
• Atom Count: 2241 
• 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


• 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: 1.964 Å
• R-Value Free: 0.229 
• R-Value Work: 0.196 

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:  
  5DHJ, 5DGZ


• 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: 

BioMarin (Shanghai), Room 605, 780 Cailun Road, Pudong District, Shanghai 201203, China.,Biogen Idec, 12 Cambridge Center, Cambridge, MA 02142, United States.,Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States.,Juno Therapeutics, 307 Westlake Ave North, Seattle, WA 98109, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Serine/threonine-protein kinase pim-1	A	299	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
5E6	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
5E6	Ki: 0.4 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.964 Å
• R-Value Free: 0.229 
• R-Value Work: 0.196 
• Space Group: P 6₅

Unit Cell:

Length (Å)	Angle (°)
a = 97.079	α = 90.00
b = 97.079	β = 90.00
c = 80.687	γ = 120.00

Software Package:

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

Structure Validation

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
  Type: Database references