2X4Z

Crystal Structure of the Human p21-Activated Kinase 4 in Complex with PF-03758309


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Small-Molecule P21-Activated Kinase Inhibitor Pf- 3758309 is a Potent Inhibitor of Oncogenic Signaling and Tumor Growth.

Murray, B.Guo, C.Piraino, J.Westwick, J.Zhang, C.Lamerdin, J.Dagostino, E.Knighton, D.R.Loi, C.-M.Zager, M.Kraynov, E.Popoff, I.Christensen, J.Martinez, R.Kephart, S.Marakovits, J.Karlicek, S.Bergqvist, S.Smeal, T.

(2010) Proc.Natl.Acad.Sci.USA 107: 9446

  • DOI: 10.1073/pnas.0911863107

  • PubMed Abstract: 
  • Despite abundant evidence that aberrant Rho-family GTPase activation contributes to most steps of cancer initiation and progression, there is a dearth of inhibitors of their effectors (e.g., p21-activated kinases). Through high-throughput screening a ...

    Despite abundant evidence that aberrant Rho-family GTPase activation contributes to most steps of cancer initiation and progression, there is a dearth of inhibitors of their effectors (e.g., p21-activated kinases). Through high-throughput screening and structure-based design, we identify PF-3758309, a potent (K(d) = 2.7 nM), ATP-competitive, pyrrolopyrazole inhibitor of PAK4. In cells, PF-3758309 inhibits phosphorylation of the PAK4 substrate GEF-H1 (IC(50) = 1.3 nM) and anchorage-independent growth of a panel of tumor cell lines (IC(50) = 4.7 +/- 3 nM). The molecular underpinnings of PF-3758309 biological effects were characterized using an integration of traditional and emerging technologies. Crystallographic characterization of the PF-3758309/PAK4 complex defined determinants of potency and kinase selectivity. Global high-content cellular analysis confirms that PF-3758309 modulates known PAK4-dependent signaling nodes and identifies unexpected links to additional pathways (e.g., p53). In tumor models, PF-3758309 inhibits PAK4-dependent pathways in proteomic studies and regulates functional activities related to cell proliferation and survival. PF-3758309 blocks the growth of multiple human tumor xenografts, with a plasma EC(50) value of 0.4 nM in the most sensitive model. This study defines PAK4-related pathways, provides additional support for PAK4 as a therapeutic target with a unique combination of functions (apoptotic, cytoskeletal, cell-cycle), and identifies a potent, orally available small-molecule PAK inhibitor with significant promise for the treatment of human cancers.


    Organizational Affiliation

    Pfizer Oncology, Pfizer, San Diego, CA 92121, USA. brion.murray@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE/THREONINE-PROTEIN KINASE PAK 4
A
296Homo sapiensMutation(s): 4 
Gene Names: PAK4 (KIAA1142)
EC: 2.7.11.1
Find proteins for O96013 (Homo sapiens)
Go to Gene View: PAK4
Go to UniProtKB:  O96013
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
X4Z
Query on X4Z

Download SDF File 
Download CCD File 
A
(3E)-N-[(1S)-2-(DIMETHYLAMINO)-1-PHENYLETHYL]-6,6-DIMETHYL-3-[(2-METHYLTHIENO[3,2-D]PYRIMIDIN-4-YL)IMINO]-4,6-DIHYDROPYRROLO[3,4-C]PYRAZOLE-5(3H)-CARBOXAMIDE
PF-0375830
C25 H28 N8 O S
JTNVXNKEXQGDNF-SQQMWKICSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
X4ZKi: 18.7 nM BINDINGMOAD
X4ZKd: 2.7 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.654α = 90.00
b = 65.923β = 90.00
c = 84.653γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance