5DEY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    5DEY, 5DFP

  • 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, we devised a mitigation strategy to address several issues such as hERG activity ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 1A, B297Homo sapiensMutation(s): 2 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
59T (Subject of Investigation/LOI)
Query on 59T

Download Ideal Coordinates CCD File 
C [auth A], D [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
59T BindingDB:  5DEY Ki: min: 3.7, max: 11 (nM) from 2 assay(s)
IC50: min: 11, max: 69 (nM) from 2 assay(s)
Binding MOAD:  5DEY Ki: 3.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.661α = 90
b = 81.863β = 106.4
c = 65.916γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



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  (Full details and data files)

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