4ZLO

Serine/threonine-protein kinase PAK1 complexed with a dibenzodiazepine: identification of an allosteric site on PAK1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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: 10.1021/acsmedchemlett.5b00102
  • Primary Citation of Related Structures:  

  • 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 strateg ...

    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.,Novartis Institutes for BioMedical Research , 5300 Chiron Way, Emeryville, California 94608, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PAK 1
A, B
297Homo sapiensMutation(s): 0 
Gene Names: PAK1
EC: 2.7.11.1
Find proteins for Q13153 (Homo sapiens)
Go to Gene View: PAK1
Go to UniProtKB:  Q13153
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
4PV
Query on 4PV

Download SDF File 
Download CCD File 
A
2,8-difluoro-11-(4-methylpiperazin-1-yl)-5H-dibenzo[b,e][1,4]diazepine
C18 H18 F2 N4
PYSIAKZWZJNMNM-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4PVIC50: 12000 - 54000 nM (100) BINDINGDB
4PVIC50: 54000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.514α = 90.00
b = 79.340β = 108.11
c = 65.789γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
REFMACphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release