6B16

P21-activated kinase 1 in complex with a 4-azaindole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.285 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Synthesis and evaluation of a series of 4-azaindole-containing p21-activated kinase-1 inhibitors.

Lee, W.Crawford, J.J.Aliagas, I.Murray, L.J.Tay, S.Wang, W.Heise, C.E.Hoeflich, K.P.La, H.Mathieu, S.Mintzer, R.Ramaswamy, S.Rouge, L.Rudolph, J.

(2016) Bioorg. Med. Chem. Lett. 26: 3518-3524

  • DOI: 10.1016/j.bmcl.2016.06.031

  • PubMed Abstract: 
  • A series of 4-azaindole-containing p21-activated kinase-1 (PAK1) inhibitors was prepared with the goal of improving physicochemical properties relative to an indole starting point. Indole 1 represented an attractive, non-basic scaffold with good PAK1 ...

    A series of 4-azaindole-containing p21-activated kinase-1 (PAK1) inhibitors was prepared with the goal of improving physicochemical properties relative to an indole starting point. Indole 1 represented an attractive, non-basic scaffold with good PAK1 affinity and cellular potency but was compromised by high lipophilicity (clogD=4.4). Azaindole 5 was designed as an indole surrogate with the goal of lowering logD and resulted in equipotent PAK1 inhibition with a 2-fold improvement in cellular potency over 1. Structure-activity relationship studies around 5 identified additional 4-azaindole analogs with superior PAK1 biochemical activity (Ki <10nM) and up to 24-fold selectivity for group I over group II PAKs. Compounds from this series showed enhanced permeability, improved aqueous solubility, and lower plasma protein binding over indole 1. The improvement in physicochemical properties translated to a 20-fold decrease in unbound clearance in mouse PK studies for azaindole 5 relative to indole 1.


    Organizational Affiliation

    Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Translational Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: wendyle@gene.com.,Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PAK 1
A, B
301Homo 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
C7Y
Query on C7Y

Download SDF File 
Download CCD File 
A, B
N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)-N~2~-[(1S)-1-(1H-pyrrolo[3,2-b]pyridin-5-yl)ethyl]pyrimidine-2,4-diamine
C19 H20 N8
GUERACYCGKAFOU-NSHDSACASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.285 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.682α = 90.00
b = 82.458β = 106.31
c = 66.036γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-09-16 
  • Released Date: 2017-10-25 
  • Deposition Author(s): Rouge, L., Wang, W.

Revision History 

  • Version 1.0: 2017-10-25
    Type: Initial release