2OBJ

Crystal structure of human PIM-1 Kinase in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2OBJ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-12-19 Released: 2007-02-06 
• Deposition Author(s): Yao, N., Cheney, I.W., Yan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.246 
• R-Value Work: 0.205 

Starting Model: experimental

Literature

Identification and structure-activity relationships of substituted pyridones as inhibitors of Pim-1 kinase.

Cheney, I.W., Yan, S., Appleby, T., Walker, H., Vo, T., Yao, N., Hamatake, R., Hong, Z., Wu, J.Z.

(2007) Bioorg Med Chem Lett 17: 1679-1683

• PubMed: 17251021 
• DOI: https://doi.org/10.1016/j.bmcl.2006.12.086
• Primary Citation of Related Structures:  
  2OBJ


• PubMed Abstract: 
  

  A novel series of highly potent substituted pyridone Pim-1 kinase inhibitors is described. Structural requirements for in vitro activity are outlined as well as a complex crystal structure with the most potent Pim-1 inhibitor reported (IC(50)=50 nM). A hydrogen bond matrix involving the Pim-1 inhibitor, two water molecules, and the catalytic core, together with a potential weak hydrogen bond between an aromatic hydrogen on the R(1) phenyl ring and a main-chain carbonyl of Pim-1, accounts for the overall potency of this inhibitor.

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Organizational Affiliation: 

Valeant Pharmaceuticals Research and Development, 3300 Hyland Avenue, Costa Mesa, CA 92626, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.35 kDa 
• Atom Count: 2,319 
• Modelled Residue Count: 273 
• Deposited Residue Count: 333 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene serine/threonine-protein kinase Pim-1	A	333	Homo sapiens	Mutation(s): 1  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VRV	B [auth A]	6-(5-BROMO-2-HYDROXYPHENYL)-2-OXO-4-PHENYL-1,2-DIHYDROPYRIDINE-3-CARBONITRILE C18 H11 Br N2 O2 SVSYJTYGPLVUOZ-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
VRV	BindingDB:  2OBJ	IC50: 50 (nM) from 1 assay(s)
	PDBBind:  2OBJ	IC50: 50 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.246 
• R-Value Work: 0.205 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.264	α = 90
b = 97.264	β = 90
c = 80.827	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-06 
Deposition Author(s): Yao, N., Cheney, I.W., Yan, S.

Revision History  

• Version 1.0: 2007-02-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary