3WE8 | pdb_00003we8

Pim-1 kinase in complex with Ruthenium-based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3WE8/pdb

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


• Deposited: 2013-07-02 Released: 2014-05-21 
• Deposition Author(s): Waehler, K., Kraeling, K., Steuber, H., Meggers, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Non-ATP-Mimetic Organometallic Protein Kinase Inhibitor

Wahler, K., Kraling, K., Steuber, H., Meggers, E.

(2013) ChemistryOpen 2: 180-185

• PubMed: 24551564 
• DOI: https://doi.org/10.1002/open.201300031
• Primary Citation of Related Structures:  
  3WE8

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Organizational Affiliation: 

Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 35043 Marburg (Germany) E-mail: [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: 31.9 kDa 
• Atom Count: 2,579 
• Modelled Residue Count: 273 
• Deposited Residue Count: 273 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	273	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RUI	B [auth A]	Cyclopentadienyl(carbon monoxide)(7-oxo-7,10-dihydro-1,8-phenanthrolin-10-yl-kappa~2~C~10~,N~1~)ruthenium C18 H7 N2 O2 Ru KWEXAKARNWEITR-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.73	α = 90
b = 97.73	β = 90
c = 81.19	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-21 
Deposition Author(s): Waehler, K., Kraeling, K., Steuber, H., Meggers, E.

Revision History  

• Version 1.0: 2014-05-21
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description