2UW9

STRUCTURE OF PKB-BETA (AKT2) COMPLEXED WITH 4-(4-chloro-phenyl)-4-(4-(1H-pyrazol-4-yl)-phenyl)-piperidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.226 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Identification of Inhibitors of Protein Kinase B Using Fragment-Based Lead Discovery.

Saxty, G.Woodhead, S.J.Berdini, V.Davies, T.G.Verdonk, M.L.Wyatt, P.G.Boyle, R.G.Barford, D.Downham, R.Garrett, M.D.Carr, R.A.

(2007) J Med Chem 50: 2293

  • DOI: 10.1021/jm070091b
  • Primary Citation of Related Structures:  
    2UW3, 2UW4, 2UW5, 2UW6, 2UW7, 2UW8, 2UW9

  • PubMed Abstract: 
  • Using fragment-based screening techniques, 5-methyl-4-phenyl-1H-pyrazole (IC50 80 microM) was identified as a novel, low molecular weight inhibitor of protein kinase B (PKB). Herein we describe the rapid elaboration of highly potent and ligand efficient analogues using a fragment growing approach ...

    Using fragment-based screening techniques, 5-methyl-4-phenyl-1H-pyrazole (IC50 80 microM) was identified as a novel, low molecular weight inhibitor of protein kinase B (PKB). Herein we describe the rapid elaboration of highly potent and ligand efficient analogues using a fragment growing approach. Iterative structure-based design was supported by protein-ligand structure determinations using a PKA-PKB "chimera" and a final protein-ligand structure of a lead compound in PKBbeta itself.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RAC-BETA SERINE/THREONINE-PROTEIN KINASEA342Homo sapiensMutation(s): 0 
Gene Names: AKT2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P31751 (Homo sapiens)
Explore P31751 
Go to UniProtKB:  P31751
PHAROS:  P31751
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31751
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCOGEN SYNTHASE KINASE-3 BETAB [auth C]10Homo sapiensMutation(s): 0 
Gene Names: GSK3B
EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49841 (Homo sapiens)
Explore P49841 
Go to UniProtKB:  P49841
PHAROS:  P49841
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49841
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GVP
Query on GVP

Download Ideal Coordinates CCD File 
C [auth A]4-(4-CHLOROPHENYL)-4-[4-(1H-PYRAZOL-4-YL)PHENYL]PIPERIDINE
C20 H20 Cl N3
LZMOSYUFVYJEPY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
GVP BindingDB:  2UW9 IC50: 18 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.058α = 90
b = 61.046β = 90
c = 132.737γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance