5KCX

Pim-1 kinase in Complex with a Selective N-substituted 7-azaindole Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5KCX/pdb

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


• Deposited: 2016-06-07 Released: 2017-07-19 
• Deposition Author(s): Mechin, I., McLean, L.R., Zhang, Y., Wang, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.180 (DCC) 

Literature

Discovery of N-substituted 7-azaindoles as PIM1 kinase inhibitors - Part I.

Barberis, C., Moorcroft, N., Arendt, C., Levit, M., Moreno-Mazza, S., Batchelor, J., Mechin, I., Majid, T.

(2017) Bioorg Med Chem Lett 27: 4730-4734

• PubMed: 28947155 
• DOI: https://doi.org/10.1016/j.bmcl.2017.08.069
• Primary Citation of Related Structures:  
  5KCX, 5TEL, 5TEX, 5TOE, 5TUR


• PubMed Abstract: 
  

  Novel N-substituted azaindoles have been discovered as PIM1 inhibitors. X-ray structures have played a significant role in orienting the chemistry effort in the initial phase of hit confirmation. Disclosure of an unconventional binding mode for 1 and 2, as demonstrated by X-ray crystallography, is presented and was an important factor in selecting and advancing a lead series.

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Organizational Affiliation: 

IDD Medicinal Chemistry, Sanofi Genzyme, 153 Second Avenue, Waltham MA 02451, USA. Electronic address: [e-mail].

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: 34.13 kDa 
• Atom Count: 2,431 
• Modelled Residue Count: 272 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	291	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6S3	D [auth A]	4-chloranyl-1-methyl-2-[4-(4-methylpiperazin-1-yl)phenyl]pyrrolo[2,3-b]pyridine-6-carboxamide C20 H22 Cl N5 O ZHUIPHDJCHSZFK-UHFFFAOYSA-N
IMD	B [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
6S3	BindingDB:  5KCX	IC50: min: 200, max: 250 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.180 (DCC) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.01	α = 90
b = 98.01	β = 90
c = 80.67	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-19 
Deposition Author(s): Mechin, I., McLean, L.R., Zhang, Y., Wang, R.

Revision History  

• Version 1.0: 2017-07-19
  Type: Initial release
  
• Version 1.1: 2017-10-18
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references