2PE1

CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) {2-Oxo-3-[1-(1H-pyrrol-2-yl)-eth-(Z)-ylidene]-2,3-dihydro-1H-indol-5-yl}-urea {BX-517} COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb2PE1/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): Yes 


• Deposited: 2007-04-01 Released: 2007-06-12 
• Deposition Author(s): Whitlow, M., Adler, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.282 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 

Literature

Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 1: Design, synthesis and biological activity.

Islam, I., Bryant, J., Chou, Y.L., Kochanny, M.J., Lee, W., Phillips, G.B., Yu, H., Adler, M., Whitlow, M., Ho, E., Lentz, D., Polokoff, M.A., Subramanyam, B., Wu, J.M., Zhu, D., Feldman, R.I., Arnaiz, D.O.

(2007) Bioorg Med Chem Lett 17: 3814-3818

• PubMed: 17531483 
• DOI: https://doi.org/10.1016/j.bmcl.2007.04.071
• Primary Citation of Related Structures:  
  2PE0, 2PE1


• PubMed Abstract: 
  

  HTS screening identified 1 with micromolar inhibitory activity against PDK1. Optimization of 1 afforded 4i (BX-517) which has single-digit nanomolar activity against PDK1 and excellent selectivity against PKA.

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Organizational Affiliation: 

Berlex Biosciences, 2600 Hilltop Dr. Richmond, CA 94804, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.97 kDa 
• Atom Count: 2,402 
• Modelled Residue Count: 276 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-phosphoinositide-dependent protein kinase 1	A	286	Homo sapiens	Mutation(s): 1  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
517	D [auth A]	1-{2-OXO-3-[(1R)-1-(1H-PYRROL-2-YL)ETHYL]-2H-INDOL-5-YL}UREA C15 H14 N4 O2 KJDBLWKTHMHALD-QMMMGPOBSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], G [auth A], H [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
517	PDBBind:  2PE1	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 0.282 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.234	α = 90
b = 125.234	β = 90
c = 47.696	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
XTALVIEW	refinement
X-GEN	data reduction
X-GEN	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-12 
Deposition Author(s): Whitlow, M., Adler, M.

Revision History  

• Version 1.0: 2007-06-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance