4ZJI

PAK1 in complex with 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

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Ligand Structure Quality Assessment 


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Literature

Optimization of a Dibenzodiazepine Hit to a Potent and Selective Allosteric PAK1 Inhibitor.

Karpov, A.S., Amiri, P., Bellamacina, C., Bellance, M.H., Breitenstein, W., Daniel, D., Denay, R., Fabbro, D., Fernandez, C., Galuba, I., Guerro-Lagasse, S., Gutmann, S., Hinh, L., Jahnke, W., Klopp, J., Lai, A., Lindvall, M.K., Ma, S., Mobitz, H., Pecchi, S., Rummel, G., Shoemaker, K., Trappe, J., Voliva, C., Cowan-Jacob, S.W., Marzinzik, A.L.

(2015) ACS Med Chem Lett 6: 776-781

  • DOI: https://doi.org/10.1021/acsmedchemlett.5b00102
  • Primary Citation of Related Structures:  
    4ZJI, 4ZJJ, 4ZLO

  • PubMed Abstract: 

    • The discovery of inhibitors targeting novel allosteric kinase sites is very challenging. Such compounds, however, once identified could offer exquisite levels of selectivity across the kinome. Herein we report our structure-based optimization strategy of a dibenzodiazepine hit 1, discovered in a fragment-based screen, yielding highly potent and selective inhibitors of PAK1 such as 2 and 3 ...

    The discovery of inhibitors targeting novel allosteric kinase sites is very challenging. Such compounds, however, once identified could offer exquisite levels of selectivity across the kinome. Herein we report our structure-based optimization strategy of a dibenzodiazepine hit 1, discovered in a fragment-based screen, yielding highly potent and selective inhibitors of PAK1 such as 2 and 3. Compound 2 was cocrystallized with PAK1 to confirm binding to an allosteric site and to reveal novel key interactions. Compound 3 modulated PAK1 at the cellular level and due to its selectivity enabled valuable research to interrogate biological functions of the PAK1 kinase.

    Organizational Affiliation: 

    Novartis Institutes for BioMedical Research , Novartis Campus, CH-4056 Basel, Switzerland.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 1
A, B, C, D
299Homo sapiensMutation(s): 0 
Gene Names: PAK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13153 (Homo sapiens)
Explore Q13153 
Go to UniProtKB:  Q13153
PHAROS:  Q13153
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13153
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4OQ
Query on 4OQ
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
I [auth D]		2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepine
C20 H22 Cl F N4
NQBRFDSRSGHBBK-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
H [auth C],
J [auth D]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
4OQ Binding MOAD:  4ZJI Kd: 340 (nM) from 1 assay(s)
BindingDB:  4ZJI Kd: min: 340, max: 4.00e+4 (nM) from 3 assay(s)
IC50: 323 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.52α = 90
b = 115.06β = 90
c = 116.36γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-07-29
    Changes: Database references