5KCX | pdb_00005kcx

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), 0.205 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.185 (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 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].
IDD Medicinal Chemistry, Sanofi Genzyme, 153 Second Avenue, Waltham MA 02451, USA.
Oncology Biochemistry/Biology, Sanofi Genzyme, 270 Albany Street, Cambridge, MA 02139, USA.
IDD In Vitro Biology, Sanofi, 153 Second Avenue, Waltham MA 02451, USA.
IDD Medicinal Chemistry, Sanofi Genzyme, 153 Second Avenue, Waltham MA 02451, USA; Program Management, Sanofi Genzyme, 49 New York Avenue, Framingham MA 01701, USA.

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 
• Modeled 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), 0.205 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.185 (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