Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.91 kDa 
• Atom Count: 2415 
• Modelled Residue Count: 274 
• Deposited Residue Count: 320 
• Unique protein chains: 2

3MA3

Crystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and a naphtho-difuran ligand

• DOI: 10.2210/pdb3MA3/pdb

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


• Deposited: 2010-03-23 Released: 2010-04-14 
• Deposition Author(s): Filippakopoulos, P., Bullock, A., Fedorov, O., Vollmar, M., von Delft, F., Cochet, C., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.233 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 

Literature

New potent dual inhibitors of CK2 and Pim kinases: discovery and structural insights.

Lopez-Ramos, M., Prudent, R., Moucadel, V., Sautel, C.F., Barette, C., Lafanechere, L., Mouawad, L., Grierson, D., Schmidt, F., Florent, J.C., Filippakopoulos, P., Bullock, A.N., Knapp, S., Reiser, J.B., Cochet, C.

(2010) FASEB J 24: 3171-3185

• PubMed: 20400536 
• DOI: 10.1096/fj.09-143743
• Primary Citation of Related Structures:  
  3MA3, 3MB6, 3MB7


• PubMed Abstract: 
  

Protein kinase casein kinase 2 (CK2) is a serine/threonine kinase with evidence of implication in growth dysregulation and apoptosis resistance, making it a relevant target for cancer therapy. Several CK2 inhibitors have been developed showing variable efficiency, emphasizing the need to expand the chemical diversity of those inhibitors. We report the identification and characterization of 2,8-difurandicarboxylic acid derivatives as a new class of nanomolar ATP-competitive inhibitors. Selectivity profiling pointed out proviral insertion Moloney virus kinases (Pim kinases) as the only other kinases that are significantly inhibited. By combining structure-activity relationship analysis with structural determination, we were able to determine the binding mode of these inhibitors for both kinases and to explain their strong inhibitory potency. Essential chemical features necessary for activity on both kinases were then identified. The described compounds are not cell permeable: however, they could provide a lead for developing novel inhibitors usable also in vivo. Given the similar but not redundant pathophysiological functions of CK2 and Pim family members, such inhibitors would provide new attractive leads for targeted cancer therapy. This work highlights that 2 functionally related kinases from different kinome branches display exquisite sensitivity to a common inhibitor.

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Organizational Affiliation: 

Centre de Recherche, Institut Curie, Paris, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene serine/threonine-protein kinase pim-1	A	313	Homo sapiens	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pimtide	B	7	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
01I (Subject of Investigation/LOI)	C [auth A]	naphtho[2,1-b:7,6-b']difuran-2,8-dicarboxylic acid C16 H8 O6 IPFSIVVOJSEJOL-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
01I	PDBBind:  3MA3	IC50: 60 (nM) from 1 assay(s)
	Binding MOAD:  3MA3	IC50: 60 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.233 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.707	α = 90
b = 97.707	β = 90
c = 80.581	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2010-03-23 
• Released Date: 2010-04-14 
Deposition Author(s): Filippakopoulos, P., Bullock, A., Fedorov, O., Vollmar, M., von Delft, F., Cochet, C., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description