3PWY | pdb_00003pwy

Crystal structure of an extender (SPD28345)-modified human PDK1 complex 2

• PDB DOI: https://doi.org/10.2210/pdb3PWY/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2010-12-09 Released: 2011-04-20 
• Deposition Author(s): Elling, R.A., Penny, D.M., Simmons, R.L., Erlanson, D.A., Romanowski, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.276 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Discovery of a potent and highly selective PDK1 inhibitor via fragment-based drug discovery.

Erlanson, D.A., Arndt, J.W., Cancilla, M.T., Cao, K., Elling, R.A., English, N., Friedman, J., Hansen, S.K., Hession, C., Joseph, I., Kumaravel, G., Lee, W.C., Lind, K.E., McDowell, R.S., Miatkowski, K., Nguyen, C., Nguyen, T.B., Park, S., Pathan, N., Penny, D.M., Romanowski, M.J., Scott, D., Silvian, L., Simmons, R.L., Tangonan, B.T., Yang, W., Sun, L.

(2011) Bioorg Med Chem Lett 21: 3078-3083

• PubMed: 21459573 
• DOI: https://doi.org/10.1016/j.bmcl.2011.03.032
• Primary Citation Related Structures: 
  3PWY, 3QC4


• PubMed Abstract: 
  

  We report the use of a fragment-based lead discovery method, Tethering with extenders, to discover a pyridinone fragment that binds in an adaptive site of the protein PDK1. With subsequent medicinal chemistry, this led to the discovery of a potent and highly selective inhibitor of PDK1, which binds in the 'DFG-out' conformation.

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Organizational Affiliation: 
• Sunesis Pharmaceuticals, Inc., 395 Oyster Point Blvd., South San Francisco, CA 94080, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.73 kDa 
• Atom Count: 2,283 
• Modeled Residue Count: 281 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-phosphoinositide-dependent protein kinase 1	A	311	Homo sapiens	Mutation(s): 2  Gene Names: PDK1, PDPK1 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SYP	B [auth A]	N-[2-({6-[(2-sulfanylethyl)amino]pyrimidin-4-yl}amino)ethyl]propanamide C11 H19 N5 O S MXLYIGOSAJROJY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.276 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.376	α = 90
b = 122.376	β = 90
c = 47.632	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-20 
Deposition Author(s): Elling, R.A., Penny, D.M., Simmons, R.L., Erlanson, D.A., Romanowski, M.J.

Revision History  

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary