4APP

Crystal Structure of the Human p21-Activated Kinase 4 in Complex with (S)-N-(5-(3-benzyl-1-methylpiperazine-4-carbonyl)-6,6-dimethyl-1,4,5, 6-tetrahydropyrrolo(3,4-c)pyrazol-3-yl)-3-phenoxybenzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of Pyrroloaminopyrazoles as Novel Pak Inhibitors.

Guo, C.Mcalpine, I.Zhang, J.Knighton, D.D.Kephart, S.Johnson, M.C.Li, H.Bouzida, D.Yang, A.Dong, L.Marakovits, J.Tikhe, J.Richardson, P.Guo, L.C.Kania, R.Edwards, M.P.Kraynov, E.Christensen, J.Piraino, J.Lee, J.Dagostino, E.Del-Carmen, C.Deng, Y.L.Smeal, T.Murray, B.W.

(2012) J Med Chem 55: 4728

  • DOI: 10.1021/jm300204j
  • Primary Citation of Related Structures:  
    4APP

  • PubMed Abstract: 
  • The P21-activated kinases (PAK) are emerging antitumor therapeutic targets. In this paper, we describe the discovery of potent PAK inhibitors guided by structure-based drug design. In addition, the efflux of the pyrrolopyrazole series was effectively reduced by applying multiple medicinal chemistry strategies, leading to a series of PAK inhibitors that are orally active in inhibiting tumor growth in vivo ...

    The P21-activated kinases (PAK) are emerging antitumor therapeutic targets. In this paper, we describe the discovery of potent PAK inhibitors guided by structure-based drug design. In addition, the efflux of the pyrrolopyrazole series was effectively reduced by applying multiple medicinal chemistry strategies, leading to a series of PAK inhibitors that are orally active in inhibiting tumor growth in vivo.


    Organizational Affiliation

    Pfizer Global Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States. alexguo01@gmail.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE PAK 4A296Homo sapiensMutation(s): 0 
Gene Names: PAK4KIAA1142
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O96013 (Homo sapiens)
Explore O96013 
Go to UniProtKB:  O96013
PHAROS:  O96013
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N53 (Subject of Investigation/LOI)
Query on N53

Download Ideal Coordinates CCD File 
B [auth A]N-[6,6-dimethyl-5-[(2S)-4-methyl-2-(phenylmethyl)piperazin-1-yl]carbonyl-2,4-dihydropyrrolo[3,4-c]pyrazol-3-yl]-3-phenoxy-benzamide
C33 H36 N6 O3
VGRHRLOVUZTBHT-VWLOTQADSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
N53 PDBBind:  4APP Ki: 64 (nM) from 1 assay(s)
Binding MOAD:  4APP Ki: 64 (nM) from 1 assay(s)
BindingDB:  4APP Ki: 64 (nM) from 1 assay(s)
EC50: 810 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.424α = 90
b = 64.995β = 90
c = 85.829γ = 90
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other