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 (Depositor), 0.308 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GVPClick on this verticalbar to view details

This is version 1.3 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: https://doi.org/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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RAC-BETA SERINE/THREONINE-PROTEIN KINASE342Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000105221 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31751
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GLYCOGEN SYNTHASE KINASE-3 BETAB [auth C]10Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000082701 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49841
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / 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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
GVP BindingDB:  2UW9 IC50: min: 17, max: 18 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.305 (Depositor), 0.308 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GVPClick on this verticalbar to view details

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
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary