Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.03 kDa 
• Atom Count: 2398 
• Residue Count: 275 
• Unique protein chains: 1

3QCY

Phosphoinositide-Dependent Kinase-1 (PDK1) kinase domain with 4-[2-Amino-6-(3-amino-1H-indazol-6-yl)-4-pyrimidinyl]-N-phenyl-2-morpholinecarboxamide

• DOI: 10.2210/pdb3QCY/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-01-17 Released: 2011-03-09 
• Deposition Author(s): Medina, J.R., Becker, C.J., Blackledge, C.W., Duquenne, C., Feng, Y., Grant, S.W., Heerding, D., Li, W.H., Miller, W.H., Romeril, S.P., Scherzer, D., Shu, A., Bobko, M.A., Chadderton, A.R., Dumble, M., Gradiner, C.M., Gilbert, S., Liu, Q., Rabindran, S.K., Sudakin, V., Xiang, H., Brady, P.G., Campobasso, N., Ward, P., Axten, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.212 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 

Literature

Structure-Based Design of Potent and Selective 3-Phosphoinositide-Dependent Kinase-1 (PDK1) Inhibitors.

Medina, J.R., Becker, C.J., Blackledge, C.W., Duquenne, C., Feng, Y., Grant, S.W., Heerding, D., Li, W.H., Miller, W.H., Romeril, S.P., Scherzer, D., Shu, A., Bobko, M.A., Chadderton, A.R., Dumble, M., Gardiner, C.M., Gilbert, S., Liu, Q., Rabindran, S.K., Sudakin, V., Xiang, H., Brady, P.G., Campobasso, N., Ward, P., Axten, J.M.

(2011) J Med Chem 54: 1871-1895

• PubMed: 21341675 
• DOI: 10.1021/jm101527u
• Primary Citation of Related Structures:  
  3QCX, 3QCY, 3QD0, 3QCQ, 3QD3, 3QCS, 3QD4


• PubMed Abstract: 
  

Phosphoinositide-dependent protein kinase-1(PDK1) is a master regulator of the AGC family of kinases and an integral component of the PI3K/AKT/mTOR pathway. As this pathway is among the most commonly deregulated across all cancers, a selective inhibitor of PDK1 might have utility as an anticancer agent. Herein we describe our lead optimization of compound 1 toward highly potent and selective PDK1 inhibitors via a structure-based design strategy. The most potent and selective inhibitors demonstrated submicromolar activity as measured by inhibition of phosphorylation of PDK1 substrates as well as antiproliferative activity against a subset of AML cell lines. In addition, reduction of phosphorylation of PDK1 substrates was demonstrated in vivo in mice bearing OCl-AML2 xenografts. These observations demonstrate the utility of these molecules as tools to further delineate the biology of PDK1 and the potential pharmacological uses of a PDK1 inhibitor.

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Related Citations: 

• Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery
  Medina, J.R., Blackledge, C.W., Heerding, D.A., Campobasso, N., Ward, P., Briand, J., Wright, L., Axten, J.M.
  (2010) ACS Med Chem Lett 1: 439

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Organizational Affiliation: 

Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-phosphoinositide-dependent protein kinase 1	A	312	Homo sapiens	Mutation(s): 0  Gene Names: PDK1, PDPK1 EC: 2.7.11.1
Find proteins for O15530 (Homo sapiens) Explore O15530  Go to UniProtKB:  O15530
NIH Common Fund Data Resources
PHAROS  O15530 GTEx  ENSG00000140992

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3Q3	A	(2S)-4-[2-amino-6-(3-amino-2H-indazol-6-yl)pyrimidin-4-yl]-N-phenylmorpholine-2-carboxamide C22 H22 N8 O2 NCSQDKMOKNQGSG-SFHVURJKSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
3Q3	IC50:  10   nM  Binding MOAD
3Q3	IC50 :  20   nM  PDBBind
3Q3	IC50:  20   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.212 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.674	α = 90
b = 123.674	β = 90
c = 47.128	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
DENZO	data reduction
PHENIX	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-01-17 
• Released Date: 2011-03-09 
Deposition Author(s): Medina, J.R., Becker, C.J., Blackledge, C.W., Duquenne, C., Feng, Y., Grant, S.W., Heerding, D., Li, W.H., Miller, W.H., Romeril, S.P., Scherzer, D., Shu, A., Bobko, M.A., Chadderton, A.R., Dumble, M., Gradiner, C.M., Gilbert, S., Liu, Q., Rabindran, S.K., Sudakin, V., Xiang, H., Brady, P.G., Campobasso, N., Ward, P., Axten, J.M.

Revision History 

• Version 1.0: 2011-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model