6VRU | pdb_00006vru

PIM-inhibitor complex 1

• PDB DOI: https://doi.org/10.2210/pdb6VRU/pdb

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


• Deposited: 2020-02-10 Released: 2020-11-04 
• Deposition Author(s): Barberis, C.E., Batchelor, J.D., Mechin, I., Liu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.202 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.183 (DCC) 

Starting Model: experimental

Literature

Discovery of SARxxxx92, a pan-PIM kinase inhibitor, efficacious in a KG1 tumor model.

Barberis, C., Erdman, P., Czekaj, M., Fire, L., Pribish, J., Tserlin, E., Maniar, S., Batchelor, J.D., Liu, J., Patel, V.F., Hebert, A., Levit, M., Wang, A., Sun, F., Huang, S.A.

(2020) Bioorg Med Chem Lett 30: 127625-127625

• PubMed: 33096160 
• DOI: https://doi.org/10.1016/j.bmcl.2020.127625
• Primary Citation Related Structures: 
  6VRU, 6VRV


• PubMed Abstract: 
  

  N-substituted azaindoles were discovered as potent pan-PIM inhibitors. Lead optimization, guided by structure and focused on physico-chemical properties allowed us to solve inherent hERG and permeability liabilities, and provided compound 27, which subsequently impacted KG-1 tumor growth in a mouse model.

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Organizational Affiliation: 
• IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States. Electronic address: [e-mail].
IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States; Present address: AbbVie, 100 Abbott Park Road, Abbott Park, IL 60064-3500, United States.
IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States.
IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States; Present address: Rakuten Medical, 11080 Roselle St, San Diego, CA 92121, United States.
Present address: Qiagen, 561 Virginia Road, Concord, MA 01742, United States.
Present address: TME Therapeutics, 3 Mossy Lane, Acton, MA 01720, United States.
Oncology Biochemistry, Sanofi, 270 Albany Street, Cambridge MA 02139, United States.
Oncology Biology, Sanofi, 270 Albany Street, Cambridge MA 02139, United States.
Oncology Pharmacology, Sanofi, 640 Memorial Drive, Cambridge MA 02139, United States.
Oncology Biology, Sanofi, 270 Albany Street, Cambridge MA 02139, United States; Present address: Bristol-Myers Squibb, 3551 Lawrenceville Princeton, Lawrence Township, NJ 08648, United States.

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: 32.1 kDa 
• Atom Count: 2,574 
• Modeled Residue Count: 273 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	274	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
ROY (Subject of Investigation/LOI)	C [auth A]	3,4-dichloro-2-cyclopropyl-1-[(piperidin-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridine-6-carboxamide C17 H20 Cl2 N4 O LYLJXIKZRAZYFB-UHFFFAOYSA-N
IMD	B [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.202 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.183 (DCC) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.555	α = 90
b = 98.555	β = 90
c = 81.009	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-04 
Deposition Author(s): Barberis, C.E., Batchelor, J.D., Mechin, I., Liu, J.

Revision History  

• Version 1.0: 2020-11-04
  Type: Initial release
  
• Version 1.1: 2020-11-25
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description