4A7C | pdb_00004a7c

Crystal structure of PIM1 kinase with ETP46546

• PDB DOI: https://doi.org/10.2210/pdb4A7C/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-11-12 Released: 2012-02-15 
• Deposition Author(s): Mazzorana, M., Montoya, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Hit to Lead Evaluation of 1,2,3-Triazolo[4,5-B]Pyridines as Pim Kinase Inhibitors.

Pastor, J., Oyarzabal, J., Saluste, G., Alvarez, R.M., Rivero, V., Ramos, F., Cendon, E., Blanco-Aparicio, C., Ajenjo, N., Cebria, A., Albarran, M.I., Cebrian, D., Corrionero, A., Fominaya, J., Montoya, G., Mazzorana, M.

(2012) Bioorg Med Chem Lett 22: 1591

• PubMed: 22266039 
• DOI: https://doi.org/10.1016/j.bmcl.2011.12.130
• Primary Citation Related Structures: 
  4A7C


• PubMed Abstract: 
  

  PIM kinases have become targets of interest due to their association with biochemical mechanisms affecting survival, proliferation and cytokine production. 1,2,3-Triazolo[4,5-b]pyridines were identified as PIM inhibitors applying a scaffold hopping approach. Initial exploration around this scaffold and X-ray crystallographic data are hereby described.

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Organizational Affiliation: 
• Experimental Therapeutics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain. [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: 35.97 kDa 
• Atom Count: 2,459 
• Modeled Residue Count: 274 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1	A	308	Homo sapiens	Mutation(s): 0  EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
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
E46	B [auth A]	N-(piperidin-4-ylmethyl)-3-[3-(trifluoromethyloxy)phenyl]-[1,2,3]triazolo[4,5-b]pyridin-5-amine C18 H19 F3 N6 O OZAALIWIRMBCOR-UHFFFAOYSA-N
IMD	C [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.355	α = 90
b = 99.355	β = 90
c = 81.119	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Mazzorana, M., Montoya, G.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 1.1: 2012-05-23
  Changes: Other
• Version 1.2: 2015-01-14
  Changes: Non-polymer description
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary