Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 37.73 kDa 
• Atom Count: 2525 
• Modelled Residue Count: 282 
• Deposited Residue Count: 328 
• Unique protein chains: 2

3CXW

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

• PDB DOI: 10.2210/pdb3CXW/pdb

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


• Deposited: 2008-04-25 Released: 2008-07-15 
• Deposition Author(s): Filippakopoulos, P., Bullock, A., Fedorov, O., Huber, K., Bracher, F., Pike, A.C.W., Roos, A., von Delft, F., 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: 2.10 Å
• R-Value Free: 0.206 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

7,8-Dichloro-1-oxo-beta-carbolines as a Versatile Scaffold for the Development of Potent and Selective Kinase Inhibitors with Unusual Binding Modes

Huber, K., Brault, L., Fedorov, O., Gasser, C., Filippakopoulos, P., Bullock, A.N., Fabbro, D., Trappe, J., Schwaller, J., Knapp, S., Bracher, F.

(2012) J Med Chem 55: 403-413

• PubMed: 22136433 
• DOI: 10.1021/jm201286z
• Primary Citation of Related Structures:  
  3BHY, 3CXW, 3CY2


• PubMed Abstract: 
  

Development of both potent and selective kinase inhibitors is a challenging task in modern drug discovery. The innate promiscuity of kinase inhibitors largely results from ATP-mimetic binding to the kinase hinge region. We present a novel class of substituted 7,8-dichloro-1-oxo-β-carbolines based on the distinct structural features of the alkaloid bauerine C whose kinase inhibitory activity does not rely on canonical ATP-mimetic hinge interactions. Intriguingly, cocrystal structures revealed an unexpected inverted binding mode and the presence of halogen bonds with kinase backbone residues. The compounds exhibit excellent selectivity over a comprehensive panel of human protein kinases while inhibiting selected kinases such as the oncogenic PIM1 at low nanomolar concentrations. Together, our biochemical and structural data suggest that this scaffold may serve as a valuable template for the design and development of specific inhibitors of various kinases including the PIM family of kinases, CLKs, DAPK3 (ZIPK), BMP2K (BIKE), and others.

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Organizational Affiliation: 

Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians University of Munich, Butenandtstrasse 5-13, 81377 Munich, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene serine/threonine-protein kinase Pim-1, Isoform 2	A	314	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pimtide peptide	B	14	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7CP	D [auth A]	(4R)-7,8-dichloro-1',9-dimethyl-1-oxo-1,2,4,9-tetrahydrospiro[beta-carboline-3,4'-piperidine]-4-carbonitrile C18 H18 Cl2 N4 O XGUIMGJMQKZRGM-LLVKDONJSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.206 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.371	α = 90
b = 98.371	β = 90
c = 81.332	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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-04-25 
• Released Date: 2008-07-15 
Deposition Author(s): Filippakopoulos, P., Bullock, A., Fedorov, O., Huber, K., Bracher, F., Pike, A.C.W., Roos, A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2012-01-18
  Changes: Database references
• Version 1.3: 2013-06-19
  Changes: Database references
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.5: 2021-10-20
  Changes: Database references, Derived calculations