3H9O

Phosphoinositide-dependent protein kinase 1 (PDK-1) in complex with compound 9

• PDB DOI: https://doi.org/10.2210/pdb3H9O/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2009-04-30 Released: 2009-08-25 
• Deposition Author(s): Olland, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.256 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

Literature

Benzo[c][2,7]naphthyridines as inhibitors of PDK-1

Kim, K.H., Wissner, A., Floyd, M.B., Fraser, H.L., Wang, Y.D., Dushin, R.G., Hu, Y., Olland, A., Guo, B., Arndt, K.

(2009) Bioorg Med Chem Lett 19: 5225-5228

• PubMed: 19628388 
• DOI: https://doi.org/10.1016/j.bmcl.2009.07.007
• Primary Citation of Related Structures:  
  3H9O


• PubMed Abstract: 
  

  A series of substituted benzo[c][2,7]-naphthyridines were prepared and showed good potency in inhibiting PDK-1. The synthesis and SAR of this series of compounds are presented as well as the X-ray crystal structure of one of these analogs in a complex with PDK-1.

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Organizational Affiliation: 

Wyeth Research, Chemical Sciences, 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: 35.95 kDa 
• Atom Count: 2,384 
• Modelled Residue Count: 276 
• 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): 0  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
9BD	B [auth A]	2-(1H-imidazol-1-yl)-9-methoxy-8-(2-methoxyethoxy)benzo[c][2,7]naphthyridin-4-amine C19 H19 N5 O3 QSSGYSRUMIOURP-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
9BD	BindingDB:  3H9O	IC50: 70 (nM) from 1 assay(s)
	PDBBind:  3H9O	IC50: 70 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.256 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.77	α = 90
b = 123.77	β = 90
c = 47.116	γ = 120

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
AMoRE	phasing
PHENIX	refinement
SAINT	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Olland, A.M.

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary