Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.91 kDa 
• Atom Count: 2467 
• Modelled Residue Count: 284 
• Deposited Residue Count: 311 
• Unique protein chains: 1

3RWQ

Discovery of a Novel, Potent and Selective Inhibitor of 3-Phosphoinositide Dependent Kinase (PDK1)

• PDB DOI: 10.2210/pdb3RWQ/pdb

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


• Deposited: 2011-05-09 Released: 2011-11-16 
• Deposition Author(s): Kazmirski, S., Kohls, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.256 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Literature

Discovery of Novel, Potent, and Selective Inhibitors of 3-Phosphoinositide-Dependent Kinase (PDK1).

Murphy, S.T., Alton, G., Bailey, S., Baxi, S.M., Burke, B.J., Chappie, T.A., Ermolieff, J., Ferre, R., Greasley, S., Hickey, M., Humphrey, J., Kablaoui, N., Kath, J., Kazmirski, S., Kraus, M., Kupchinsky, S., Li, J., Lingardo, L., Marx, M.A., Richter, D., Tanis, S.P., Tran, K., Vernier, W., Xie, Z., Yin, M.J., Yu, X.H.

(2011) J Med Chem 54: 8490-8500

• PubMed: 22040023 
• DOI: 10.1021/jm201019k
• Primary Citation of Related Structures:  
  3RWP, 3RWQ


• PubMed Abstract: 
  

Analogues substituted with various amines at the 6-position of the pyrazine ring on (4-amino-7-isopropyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)pyrazin-2-ylmethanone were discovered as potent and selective inhibitors of PDK1 with potential as anticancer agents. An early lead with 2-pyridine-3-ylethylamine as the pyrazine substituent showed moderate potency and selectivity. Structure-based drug design led to improved potency and selectivity against PI3Kα through a combination of cyclizing the ethylene spacer into a saturated, five-membered ring and substituting on the 4-position of the aryl ring with a fluorine. ADME properties were improved by lowering the lipophilicity with heteroatom replacements in the saturated, five-membered ring. The optimized analogues have a PDK1 Ki of 1 nM and >100-fold selectivity against PI3K/AKT-pathway kinases. The cellular potency of these analogues was assessed by the inhibition of AKT phosphorylation (T308) and by their antiproliferation activity against a number of tumor cell lines.

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Organizational Affiliation: 

Pfizer Global Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-phosphoinositide-dependent protein kinase 1	A	311	Homo sapiens	Mutation(s): 0  Gene Names: PDPK1, PDK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O15530 (Homo sapiens) Explore O15530  Go to UniProtKB:  O15530
PHAROS:  O15530 GTEx:  ENSG00000140992

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3RW	B [auth A]	[4-amino-7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl](6-{[2-(pyridin-3-yl)ethyl]amino}pyrazin-2-yl)methanone C21 H22 N8 O WMUOCKJUZCEMCY-UHFFFAOYSA-N
SO4	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], E [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
3RW	PDBBind:  3RWQ	Ki: 35 (nM) from 1 assay(s)
	BindingDB:  3RWQ	Ki: 35 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.256 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.213	α = 90
b = 123.213	β = 90
c = 47.424	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-09 
• Released Date: 2011-11-16 
Deposition Author(s): Kazmirski, S., Kohls, D.

Revision History  

• Version 1.0: 2011-11-16
  Type: Initial release
  
• Version 1.1: 2011-12-28
  Changes: Database references