1Z5M

Crystal Structure Of N1-[3-[[5-bromo-2-[[3-[(1-pyrrolidinylcarbonyl)amino]phenyl]amino]-4-pyrimidinyl]amino]propyl]-2,2-dimethylpropanediamide Complexed with Human PDK1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Novel small molecule inhibitors of 3-phosphoinositide-dependent kinase-1.

Feldman, R.I.Wu, J.M.Polokoff, M.A.Kochanny, M.J.Dinter, H.Zhu, D.Biroc, S.L.Alicke, B.Bryant, J.Yuan, S.Buckman, B.O.Lentz, D.Ferrer, M.Whitlow, M.Adler, M.Finster, S.Chang, Z.Arnaiz, D.O.

(2005) J Biol Chem 280: 19867-19874

  • DOI: 10.1074/jbc.M501367200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The phosphoinositide 3-kinase/3-phosphoinositide-dependent kinase 1 (PDK1)/Akt signaling pathway plays a key role in cancer cell growth, survival, and tumor angiogenesis and represents a promising target for anticancer drugs. Here, we describe three ...

    The phosphoinositide 3-kinase/3-phosphoinositide-dependent kinase 1 (PDK1)/Akt signaling pathway plays a key role in cancer cell growth, survival, and tumor angiogenesis and represents a promising target for anticancer drugs. Here, we describe three potent PDK1 inhibitors, BX-795, BX-912, and BX-320 (IC(50) = 11-30 nm) and their initial biological characterization. The inhibitors blocked PDK1/Akt signaling in tumor cells and inhibited the anchorage-dependent growth of a variety of tumor cell lines in culture or induced apoptosis. A number of cancer cell lines with elevated Akt activity were >30-fold more sensitive to growth inhibition by PDK1 inhibitors in soft agar than on tissue culture plastic, consistent with the cell survival function of the PDK1/Akt signaling pathway, which is particularly important for unattached cells. BX-320 inhibited the growth of LOX melanoma tumors in the lungs of nude mice after injection of tumor cells into the tail vein. The effect of BX-320 on cancer cell growth in vitro and in vivo indicates that PDK1 inhibitors may have clinical utility as anticancer agents.


    Related Citations: 
    • High Resolution Crystal Structure of the Human Pdk1 Catalytic Domain Defines the Regulatory Phosphopeptide Docking Site
      Biondi, R.M., Komander, D., Thomas, C.C., Lizcano, J.M., Deak, M., Alessi, D.R., Van Aalten, D.M.F.
      (2002) EMBO J 21: 4219

    Organizational Affiliation

    Departments of Cancer Research, Berlex Biosciences, Richmond, California 94804, USA. rick_feldman@berlex.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-phosphoinositide dependent protein kinase-1
A
286Homo sapiensMutation(s): 1 
Gene Names: PDPK1PDK1
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
Find proteins for O15530 (Homo sapiens)
Go to UniProtKB:  O15530
NIH Common Fund Data Resources
PHAROS  O15530
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LI8
Query on LI8

Download CCD File 
A
N-(3-{[5-BROMO-2-({3-[(PYRROLIDIN-1-YLCARBONYL)AMINO]PHENYL}AMINO)PYRIMIDIN-4-YL]AMINO}PROPYL)-2,2-DIMETHYLMALONAMIDE
C23 H31 Br N8 O3
ZNSULAZTNWFKEW-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LI8IC50:  39   nM  BindingDB
LI8IC50:  30   nM  Binding MOAD
LI8IC50 :  30   nM  PDBBind
LI8IC50:  30   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.219 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.61α = 90
b = 124.61β = 90
c = 46.97γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
X-GENdata reduction
MOLREPphasing
X-PLORrefinement
X-GENdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2005-03-18 
  • Released Date: 2005-04-19 
  • Deposition Author(s): Whitlow, M., Adler, M.

Revision History 

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description