2R7B

Crystal Structure of the Phosphoinositide-dependent Kinase-1 (PDK-1)Catalytic Domain bound to a dibenzonaphthyridine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2R7B/pdb

• Classification: SIGNALING PROTEIN, TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-09-07 Released: 2008-09-09 
• Deposition Author(s): Olland, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.250 
• R-Value Work: 0.225 

Starting Model: experimental

Literature

Discovery of Dibenzo[c,f][2,7]naphthyridines as Potent and Selective 3-Phosphoinositide-Dependent Kinase-1 Inhibitors.

Gopalsamy, A., Shi, M., Boschelli, D.H., Williamson, R., Olland, A.M., Hu, Y., Krishnamurthy, G., Han, X., Arndt, K., Guo, B.

(2007) J Med Chem 50: 5547-5549

• PubMed: 17941624 
• DOI: https://doi.org/10.1021/jm070851i
• Primary Citation of Related Structures:  
  2R7B


• PubMed Abstract: 
  

  With high-throughput screening, substituted dibenzo[c,f][2,7]naphthyridine 1 was identified as a novel potent and selective phosphoinositide-dependent kinase-1 (PDK-1) inhibitor. Various regions of the lead molecule were explored to understand the SAR requirement for this scaffold. The crystal structure of 1 with kinase domain of PDK-1 confirmed the binding in the active site. The key interaction of the molecule with the active site residues, observed SAR, and the biological profile are discussed in detail.

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Organizational Affiliation: 

Chemical and Screening Sciences and Oncology, Wyeth Research, 401 N. Middletown Road, Pearl River, NY 10965, 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: 36.08 kDa 
• Atom Count: 2,304 
• Modelled Residue Count: 275 
• Deposited Residue Count: 312 
• Unique protein chains: 1

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: 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
253	C [auth A]	10,11-dimethoxy-4-methyldibenzo[c,f]-2,7-naphthyridine-3,6-diamine C19 H18 N4 O2 NVINUNQBDNEMSY-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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
253	PDBBind:  2R7B	IC50: 60 (nM) from 1 assay(s)
	BindingDB:  2R7B	IC50: 60 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.250 
• R-Value Work: 0.225 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.281	α = 90
b = 124.281	β = 90
c = 47.184	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-09 
Deposition Author(s): Olland, A.M.

Revision History  

• Version 1.0: 2008-09-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2024-03-27
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2024-11-06
  Changes: Structure summary