2OI4

Crystal structure of human PIM1 in complex with fluorinated ruthenium pyridocarbazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1039/b700433h

  • 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 i ...

    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. meggers@sas.upenn.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene serine/threonine-protein kinase Pim-1
X
313Homo sapiensGene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Go to Gene View: PIM1
Go to UniProtKB:  P11309
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
X
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
JM1
Query on JM1

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Download CCD File 
X
FLOURINATED PYRIDOCARBAZOLE CYCLOPENTADIENYL RU(CO) COMPLEX
C23 H12 F N3 O3 Ru
IGUXRLCWWSQJKI-GQABUAIVDG
 Ligand Interaction
CL
Query on CL

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Download CCD File 
X
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
X
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JM1IC50: 2.5 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.189 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 98.104α = 90.00
b = 98.104β = 90.00
c = 80.672γ = 120.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
REFMACrefinement
CrystalCleardata collection
CrystalCleardata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2007-11-14
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance