5DEY

Crystal structure of PAK1 in complex with an inhibitor compound G-5555


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design of Selective PAK1 Inhibitor G-5555: Improving Properties by Employing an Unorthodox Low-pK a Polar Moiety.

Ndubaku, C.O.Crawford, J.J.Drobnick, J.Aliagas, I.Campbell, D.Dong, P.Dornan, L.M.Duron, S.Epler, J.Gazzard, L.Heise, C.E.Hoeflich, K.P.Jakubiak, D.La, H.Lee, W.Lin, B.Lyssikatos, J.P.Maksimoska, J.Marmorstein, R.Murray, L.J.O'Brien, T.Oh, A.Ramaswamy, S.Wang, W.Zhao, X.Zhong, Y.Blackwood, E.Rudolph, J.

(2015) Acs Med.Chem.Lett. 6: 1241-1246

  • DOI: 10.1021/acsmedchemlett.5b00398
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Signaling pathways intersecting with the p21-activated kinases (PAKs) play important roles in tumorigenesis and cancer progression. By recognizing that the limitations of FRAX1036 (1) were chiefly associated with the highly basic amine it contained, ...

    Signaling pathways intersecting with the p21-activated kinases (PAKs) play important roles in tumorigenesis and cancer progression. By recognizing that the limitations of FRAX1036 (1) were chiefly associated with the highly basic amine it contained, we devised a mitigation strategy to address several issues such as hERG activity. The 5-amino-1,3-dioxanyl moiety was identified as an effective means of reducing pK a and logP simultaneously. When positioned properly within the scaffold, this group conferred several benefits including potency, pharmacokinetics, and selectivity. Mouse xenograft PK/PD studies were carried out using an advanced compound, G-5555 (12), derived from this approach. These studies concluded that dose-dependent pathway modulation was achievable and paves the way for further in vivo investigations of PAK1 function in cancer and other diseases.


    Organizational Affiliation

    Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, 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): 2 
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
59T
Query on 59T

Download SDF File 
Download CCD File 
A, B
8-[(trans-5-amino-1,3-dioxan-2-yl)methyl]-6-[2-chloro-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one
C25 H25 Cl N6 O3
ZBCMHWUFWQFPLV-VVOJOOEHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
59TKi: 3.7 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.661α = 90.00
b = 81.863β = 106.40
c = 65.916γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-08-26 
  • Released Date: 2016-01-27 
  • Deposition Author(s): Oh, A., Tam, C., Wang, W.

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Data collection