2OI4 | pdb_00002oi4

Crystal structure of human PIM1 in complex with fluorinated ruthenium pyridocarbazole

• PDB DOI: https://doi.org/10.2210/pdb2OI4/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2007-01-10 Released: 2007-04-10 
• Deposition Author(s): Maksimoska, J., Meggers, E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Ruthenium half-sandwich complexes as protein kinase inhibitors: derivatization of the pyridocarbazole pharmacophore ligand.

Pagano, N., Maksimoska, J., Bregman, H., Williams, D.S., Webster, R.D., Xue, F., Meggers, E.

(2007) Org Biomol Chem 5: 1218-1227

• PubMed: 17406720 
• DOI: https://doi.org/10.1039/b700433h
• Primary Citation Related Structures: 
  2OI4


• PubMed Abstract: 
  

  A general route to ruthenium pyridocarbazole half-sandwich complexes is presented and applied to the synthesis of sixteen new compounds, many of which have modulated protein kinase inhibition properties. For example, the incorporation of a fluorine into the pyridine moiety increases the binding affinity for glycogen synthase kinase 3 by almost one order of magnitude. These data are supplemented with cyclic voltammetry experiments and a protein co-crystallographic study.

---

Organizational Affiliation: 
• Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, 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: 36.59 kDa 
• Atom Count: 2,477 
• Modeled Residue Count: 275 
• Deposited Residue Count: 313 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene serine/threonine-protein kinase Pim-1	A [auth X]	313	Homo sapiens	Mutation(s): 1  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JM1	C [auth X]	FLUORINATED PYRIDOCARBAZOLE CYCLOPENTADIENYL RU(CO) COMPLEX C23 H12 F N3 O3 Ru IGUXRLCWWSQJKI-UHFFFAOYSA-M
EPE	G [auth X]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
EDO	D [auth X], E [auth X], F [auth X]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	B [auth X]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.104	α = 90
b = 98.104	β = 90
c = 80.672	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-10 
Deposition Author(s): Maksimoska, J., Meggers, E.

Revision History  

• Version 1.0: 2007-04-10
  Type: Initial release
  
• Version 1.1: 2007-11-14
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-25
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.4: 2021-10-20
  Changes: Advisory, Database references, Derived calculations
• Version 1.5: 2023-12-27
  Changes: Data collection